diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index f4190aa72c..113ac0e553 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -427,11 +427,20 @@ void EmuThread()
 		Keyboard::Initialize(s_window_handle);
 		init_controllers = true;
 	}
+	else
+	{
+		// Update references in case controllers were refreshed
+		Pad::LoadConfig();
+		Keyboard::LoadConfig();
+	}
 
 	// Load and Init Wiimotes - only if we are booting in Wii mode
 	if (core_parameter.bWii)
 	{
-		Wiimote::Initialize(s_window_handle, !s_state_filename.empty());
+		if (init_controllers)
+			Wiimote::Initialize(s_window_handle, !s_state_filename.empty());
+		else
+			Wiimote::LoadConfig();
 
 		// Activate Wiimotes which don't have source set to "None"
 		for (unsigned int i = 0; i != MAX_BBMOTES; ++i)
diff --git a/Source/Core/Core/HW/GCKeyboard.cpp b/Source/Core/Core/HW/GCKeyboard.cpp
index 1e57e8e802..d6ac24e637 100644
--- a/Source/Core/Core/HW/GCKeyboard.cpp
+++ b/Source/Core/Core/HW/GCKeyboard.cpp
@@ -45,6 +45,11 @@ void Initialize(void* const hwnd)
 	s_config.LoadConfig(true);
 }
 
+void LoadConfig()
+{
+	s_config.LoadConfig(true);
+}
+
 void GetStatus(u8 _port, KeyboardStatus* _pKeyboardStatus)
 {
 	memset(_pKeyboardStatus, 0, sizeof(*_pKeyboardStatus));
@@ -52,19 +57,6 @@ void GetStatus(u8 _port, KeyboardStatus* _pKeyboardStatus)
 
 	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
 
-	if (!lk.owns_lock())
-	{
-		// if gui has lock (messing with controls), skip this input cycle
-		// center axes and return
-		_pKeyboardStatus->key0x = 0;
-		_pKeyboardStatus->key1x = 0;
-		_pKeyboardStatus->key2x = 0;
-		_pKeyboardStatus->key3x = 0;
-		_pKeyboardStatus->key4x = 0;
-		_pKeyboardStatus->key5x = 0;
-		return;
-	}
-
 	// get input
 	((GCKeyboard*)s_config.controllers[_port])->GetInput(_pKeyboardStatus);
 }
diff --git a/Source/Core/Core/HW/GCKeyboard.h b/Source/Core/Core/HW/GCKeyboard.h
index 407b822db1..f535567381 100644
--- a/Source/Core/Core/HW/GCKeyboard.h
+++ b/Source/Core/Core/HW/GCKeyboard.h
@@ -13,6 +13,7 @@ namespace Keyboard
 
 void Shutdown();
 void Initialize(void* const hwnd);
+void LoadConfig();
 
 InputConfig* GetConfig();
 
diff --git a/Source/Core/Core/HW/GCPad.cpp b/Source/Core/Core/HW/GCPad.cpp
index 34ae9ea618..b57a6d02f2 100644
--- a/Source/Core/Core/HW/GCPad.cpp
+++ b/Source/Core/Core/HW/GCPad.cpp
@@ -46,6 +46,12 @@ void Initialize(void* const hwnd)
 	s_config.LoadConfig(true);
 }
 
+void LoadConfig()
+{
+	s_config.LoadConfig(true);
+}
+
+
 void GetStatus(u8 _numPAD, GCPadStatus* _pPADStatus)
 {
 	memset(_pPADStatus, 0, sizeof(*_pPADStatus));
@@ -53,16 +59,6 @@ void GetStatus(u8 _numPAD, GCPadStatus* _pPADStatus)
 
 	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
 
-	if (!lk.owns_lock())
-	{
-		// if gui has lock (messing with controls), skip this input cycle
-		// center axes and return
-		_pPADStatus->stickX = GCPadStatus::MAIN_STICK_CENTER_X;
-		_pPADStatus->stickY = GCPadStatus::MAIN_STICK_CENTER_Y;
-		_pPADStatus->substickX = GCPadStatus::C_STICK_CENTER_X;
-		_pPADStatus->substickY = GCPadStatus::C_STICK_CENTER_Y;
-		return;
-	}
 
 	// get input
 	((GCPad*)s_config.controllers[_numPAD])->GetInput(_pPADStatus);
@@ -72,9 +68,6 @@ void Rumble(u8 _numPAD, const ControlState strength)
 {
 	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
 
-	if (!lk.owns_lock())
-		return;
-
 	((GCPad*)s_config.controllers[ _numPAD ])->SetOutput(strength);
 }
 
@@ -83,8 +76,6 @@ bool GetMicButton(u8 pad)
 
 	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
 
-	if (!lk.owns_lock())
-		return false;
 
 	return ((GCPad*)s_config.controllers[pad])->GetMicButton();
 }
diff --git a/Source/Core/Core/HW/GCPad.h b/Source/Core/Core/HW/GCPad.h
index d9da72e9fc..5d70f9274c 100644
--- a/Source/Core/Core/HW/GCPad.h
+++ b/Source/Core/Core/HW/GCPad.h
@@ -13,6 +13,7 @@ namespace Pad
 
 void Shutdown();
 void Initialize(void* const hwnd);
+void LoadConfig();
 
 InputConfig* GetConfig();
 
diff --git a/Source/Core/Core/HW/Wiimote.cpp b/Source/Core/Core/HW/Wiimote.cpp
index 357b3b1fea..756384ca30 100644
--- a/Source/Core/Core/HW/Wiimote.cpp
+++ b/Source/Core/Core/HW/Wiimote.cpp
@@ -55,6 +55,12 @@ void Initialize(void* const hwnd, bool wait)
 		Movie::ChangeWiiPads();
 }
 
+void LoadConfig()
+{
+	s_config.LoadConfig(true);
+}
+
+
 void Resume()
 {
 	WiimoteReal::Resume();
@@ -113,7 +119,7 @@ void Update(int _number)
 	//PanicAlert( "Wiimote_Update" );
 
 	// TODO: change this to a try_to_lock, and make it give empty input on failure
-	std::lock_guard<std::recursive_mutex> lk(s_config.controls_lock);
+	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
 
 	if (WIIMOTE_SRC_EMU & g_wiimote_sources[_number])
 		((WiimoteEmu::Wiimote*)s_config.controllers[_number])->Update();
diff --git a/Source/Core/Core/HW/Wiimote.h b/Source/Core/Core/HW/Wiimote.h
index 71fa2d28b6..81f2e83c5c 100644
--- a/Source/Core/Core/HW/Wiimote.h
+++ b/Source/Core/Core/HW/Wiimote.h
@@ -36,6 +36,7 @@ namespace Wiimote
 
 void Shutdown();
 void Initialize(void* const hwnd, bool wait = false);
+void LoadConfig();
 void Resume();
 void Pause();
 
diff --git a/Source/Core/Core/HotkeyManager.cpp b/Source/Core/Core/HotkeyManager.cpp
index 8233b32d5e..c3a6461ebe 100644
--- a/Source/Core/Core/HotkeyManager.cpp
+++ b/Source/Core/Core/HotkeyManager.cpp
@@ -6,47 +6,11 @@
 #include "Core/CoreParameter.h"
 #include "Core/HotkeyManager.h"
 
-static const u32 hotkey_bitmasks[] =
-{
-	1 << 0,
-	1 << 1,
-	1 << 2,
-	1 << 3,
-	1 << 4,
-	1 << 5,
-	1 << 6,
-	1 << 7,
-	1 << 8,
-	1 << 9,
-	1 << 10,
-	1 << 11,
-	1 << 12,
-	1 << 13,
-	1 << 14,
-	1 << 15,
-	1 << 16,
-	1 << 17,
-	1 << 18,
-	1 << 19,
-	1 << 20,
-	1 << 21,
-	1 << 22,
-	1 << 23,
-	1 << 24,
-	1 << 25,
-	1 << 26,
-	1 << 27,
-	1 << 28,
-	1 << 29,
-	1 << 30,
-	1u << 31u
-};
-
 const std::string hotkey_labels[] =
 {
-	_trans("Open"),
-	_trans("Change Disc"),
-	_trans("Refresh List"),
+	(""), // Open
+	(""), // Change Disc
+	(""), // Refresh List
 
 	_trans("Toggle Pause"),
 	_trans("Stop"),
@@ -60,7 +24,7 @@ const std::string hotkey_labels[] =
 
 	_trans("Toggle Fullscreen"),
 	_trans("Take Screenshot"),
-	_trans("Exit"),
+	(""), // Exit
 
 	_trans("Connect Wiimote 1"),
 	_trans("Connect Wiimote 2"),
@@ -153,39 +117,36 @@ const int num_hotkeys = (sizeof(hotkey_labels) / sizeof(hotkey_labels[0]));
 namespace HotkeyManagerEmu
 {
 
-static u32 hotkeyDown[6];
+static u32 hotkeyDown[3];
+static HotkeyStatus hotkey;
 
 static InputConfig s_config("Hotkeys", _trans("Hotkeys"), "Hotkeys");
+
 InputConfig* GetConfig()
 {
 	return &s_config;
 }
 
-void GetStatus(u8 _port, HotkeyStatus* _pHotkeyStatus)
+void GetStatus()
 {
-	memset(_pHotkeyStatus, 0, sizeof(*_pHotkeyStatus));
-	_pHotkeyStatus->err = PAD_ERR_NONE;
-
-	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
-
-	if (!lk.owns_lock())
-	{
-		// if gui has lock (messing with controls), skip this input cycle
-		for (int i = 0; i < 6; i++)
-			_pHotkeyStatus->button[i] = 0;
-
-		return;
-	}
+	hotkey.err = PAD_ERR_NONE;
 
 	// get input
-	((HotkeyManager*)s_config.controllers[_port])->GetInput(_pHotkeyStatus);
+	((HotkeyManager*)s_config.controllers[0])->GetInput(&hotkey);
+}
+
+bool IsEnabled()
+{
+	return enabled;
+}
+
+void Enable(bool enable_toggle)
+{
+	enabled = enable_toggle;
 }
 
 bool IsPressed(int Id, bool held)
 {
-	HotkeyStatus hotkey;
-	memset(&hotkey, 0, sizeof(hotkey));
-	GetStatus(0, &hotkey);
 	unsigned int set = Id / 32;
 	unsigned int setKey = Id % 32;
 	if (hotkey.button[set] & (1 << setKey))
@@ -215,8 +176,15 @@ void Initialize(void* const hwnd)
 	// load the saved controller config
 	s_config.LoadConfig(true);
 
-	for (unsigned int i = 0; i < 6; ++i)
+	for (unsigned int i = 0; i < 3; ++i)
 		hotkeyDown[i] = 0;
+
+	enabled = true;
+}
+
+void LoadConfig()
+{
+	s_config.LoadConfig(true);
 }
 
 void Shutdown()
@@ -235,7 +203,7 @@ void Shutdown()
 
 HotkeyManager::HotkeyManager()
 {
-	for (int set = 0; set < 6; set++)
+	for (int set = 0; set < 3; set++)
 	{
 		// buttons
 		if ((set * 32) < num_hotkeys)
@@ -243,7 +211,7 @@ HotkeyManager::HotkeyManager()
 
 		for (int key = 0; key < 32; key++)
 		{
-			if ((set * 32 + key) < num_hotkeys)
+			if ((set * 32 + key) < num_hotkeys && hotkey_labels[set * 32 + key].length() != 0)
 			{
 				m_keys[set]->controls.emplace_back(new ControlGroup::Input(hotkey_labels[set * 32 + key]));
 			}
@@ -266,284 +234,30 @@ std::string HotkeyManager::GetName() const
 
 void HotkeyManager::GetInput(HotkeyStatus* const kb)
 {
-	for (int set = 0; set < 6; set++)
+	for (int set = 0; set < 3; set++)
+	{
+		std::vector<u32> bitmasks;
+		for (int key = 0; key < 32; key++)
+		{
+			if ((set * 32 + key) < num_hotkeys && hotkey_labels[set * 32 + key].length() != 0)
+				bitmasks.push_back(1 << key);
+		}
+
 		if ((set * 32) < num_hotkeys)
-			m_keys[set]->GetState(&kb->button[set], hotkey_bitmasks);
+		{
+			kb->button[set] = 0;
+			m_keys[set]->GetState(&kb->button[set], bitmasks.data());
+		}
+	}
 }
 
 void HotkeyManager::LoadDefaults(const ControllerInterface& ciface)
 {
-#define set_control(group, num, str)  (group)->controls[num]->control_ref->expression = (str)
-
-	ControllerEmu::LoadDefaults(ciface);
-
-	// Buttons
-#ifdef _WIN32
-	set_control(m_keys[0], 0, "(LCONTROL | RCONTROL) & L"); // Open
-	set_control(m_keys[0], 1, ""); // ChangeDisc
-	set_control(m_keys[0], 2, ""); // RefreshList
-	set_control(m_keys[0], 3, "F10"); // PlayPause
-	set_control(m_keys[0], 4, "ESCAPE"); // Stop
-	set_control(m_keys[0], 5, ""); // Reset
-	set_control(m_keys[0], 6, ""); // FrameAdvance
-	set_control(m_keys[0], 7, ""); // StartRecording
-	set_control(m_keys[0], 8, ""); // PlayRecording
-	set_control(m_keys[0], 9, ""); // ExportRecording
-	set_control(m_keys[0], 10, ""); // Readonlymode
-	set_control(m_keys[0], 11, "(LMENU | RMENU) & RETURN"); // ToggleFullscreen
-	set_control(m_keys[0], 12, "`F9` & !(LMENU | RMENU)"); // Screenshot
-	set_control(m_keys[0], 13, ""); // Exit
-	set_control(m_keys[0], 14, "(LMENU | RMENU) & `F5`"); // Wiimote1Connect
-	set_control(m_keys[0], 15, "(LMENU | RMENU) & `F6`"); // Wiimote2Connect
-	set_control(m_keys[0], 16, "(LMENU | RMENU) & `F7`"); // Wiimote3Connect
-	set_control(m_keys[0], 17, "(LMENU | RMENU) & `F8`"); // Wiimote4Connect
-	set_control(m_keys[0], 18, "(LMENU | RMENU) & `F9`"); // BalanceBoardConnect
-	set_control(m_keys[0], 19, ""); // VolumeDown
-	set_control(m_keys[0], 20, ""); // VolumeUp
-	set_control(m_keys[0], 21, ""); // VolumeToggleMute
-	set_control(m_keys[0], 22, ""); // ToggleIR
-	set_control(m_keys[0], 23, ""); // ToggleAspectRatio
-	set_control(m_keys[0], 24, ""); // ToggleEFBCopies
-	set_control(m_keys[0], 25, ""); // ToggleFog
-	set_control(m_keys[0], 26, "TAB"); // ToggleThrottle
-	set_control(m_keys[0], 27, ""); // DecreaseFrameLimit
-	set_control(m_keys[0], 28, ""); // IncreaseFrameLimit
-	set_control(m_keys[0], 29, "1"); // FreelookDecreaseSpeed
-	set_control(m_keys[0], 30, "2"); // FreelookIncreaseSpeed
-	set_control(m_keys[0], 31, "F"); // FreelookResetSpeed
-	set_control(m_keys[1], 0, "E"); // FreelookUp
-	set_control(m_keys[1], 1, "Q"); // FreelookDown
-	set_control(m_keys[1], 2, "A"); // FreelookLeft
-	set_control(m_keys[1], 3, "D"); // FreelookRight
-	set_control(m_keys[1], 4, "W"); // FreelookZoomIn
-	set_control(m_keys[1], 5, "S"); // FreelookZoomOut
-	set_control(m_keys[1], 6, "R"); // FreelookReset
-	set_control(m_keys[1], 7, ""); // DecreaseDepth
-	set_control(m_keys[1], 8, ""); // IncreaseDepth
-	set_control(m_keys[1], 9, ""); // DecreaseConvergence
-	set_control(m_keys[1], 10, ""); // IncreaseConvergence
-	set_control(m_keys[1], 11, "`F1` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot1
-	set_control(m_keys[1], 12, "`F2` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot2
-	set_control(m_keys[1], 13, "`F3` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot3
-	set_control(m_keys[1], 14, "`F4` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot4
-	set_control(m_keys[1], 15, "`F5` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot5
-	set_control(m_keys[1], 16, "`F6` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot6
-	set_control(m_keys[1], 17, "`F7` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot7
-	set_control(m_keys[1], 18, "`F8` & !(LSHIFT | RSHIFT) & !(LMENU | RMENU)"); // LoadStateSlot8
-	set_control(m_keys[1], 19, ""); // LoadStateSlot9
-	set_control(m_keys[1], 20, ""); // LoadStateSlot10
-	set_control(m_keys[1], 21, "(LSHIFT | RSHIFT) & `F1`"); // SaveStateSlot1
-	set_control(m_keys[1], 22, "(LSHIFT | RSHIFT) & `F2`"); // SaveStateSlot2
-	set_control(m_keys[1], 23, "(LSHIFT | RSHIFT) & `F3`"); // SaveStateSlot3
-	set_control(m_keys[1], 24, "(LSHIFT | RSHIFT) & `F4`"); // SaveStateSlot4
-	set_control(m_keys[1], 25, "(LSHIFT | RSHIFT) & `F5`"); // SaveStateSlot5
-	set_control(m_keys[1], 26, "(LSHIFT | RSHIFT) & `F6`"); // SaveStateSlot6
-	set_control(m_keys[1], 27, "(LSHIFT | RSHIFT) & `F7`"); // SaveStateSlot7
-	set_control(m_keys[1], 28, "(LSHIFT | RSHIFT) & `F8`"); // SaveStateSlot8
-	set_control(m_keys[1], 29, ""); // SaveStateSlot9
-	set_control(m_keys[1], 30, ""); // SaveStateSlot10
-	set_control(m_keys[1], 31, ""); // SelectStateSlot1
-	set_control(m_keys[2], 0, ""); // SelectStateSlot2
-	set_control(m_keys[2], 1, ""); // SelectStateSlot3
-	set_control(m_keys[2], 2, ""); // SelectStateSlot4
-	set_control(m_keys[2], 3, ""); // SelectStateSlot5
-	set_control(m_keys[2], 4, ""); // SelectStateSlot6
-	set_control(m_keys[2], 5, ""); // SelectStateSlot7
-	set_control(m_keys[2], 6, ""); // SelectStateSlot8
-	set_control(m_keys[2], 7, ""); // SelectStateSlot9
-	set_control(m_keys[2], 8, ""); // SelectStateSlot10
-	set_control(m_keys[2], 9, ""); // SaveSelectedSlot
-	set_control(m_keys[2], 10, ""); // LoadSelectedSlot
-	set_control(m_keys[2], 11, ""); // LoadLastState1
-	set_control(m_keys[2], 12, ""); // LoadLastState2
-	set_control(m_keys[2], 13, ""); // LoadLastState3
-	set_control(m_keys[2], 14, ""); // LoadLastState4
-	set_control(m_keys[2], 15, ""); // LoadLastState5
-	set_control(m_keys[2], 16, ""); // LoadLastState6
-	set_control(m_keys[2], 17, ""); // LoadLastState7
-	set_control(m_keys[2], 18, ""); // LoadLastState8
-	set_control(m_keys[2], 19, ""); // SaveFirstState
-	set_control(m_keys[2], 20, "`F12` & !(LSHIFT | RSHIFT)"); // UndoLoadState
-	set_control(m_keys[2], 21, "(LSHIFT | RSHIFT) & `F12`"); // UndoSaveState
-	set_control(m_keys[2], 22, ""); // SaveStateFile
-	set_control(m_keys[2], 23, ""); // LoadStateFile
-#elif __APPLE__
-	set_control(m_keys[0], 0, "(`Left Command` | `Right Command`) & `O`"); // Open
-	set_control(m_keys[0], 1, ""); // ChangeDisc
-	set_control(m_keys[0], 2, ""); // RefreshList
-	set_control(m_keys[0], 3, "(`Left Command` | `Right Command`) & `P`"); // PlayPause
-	set_control(m_keys[0], 4, "(`Left Command` | `Right Command`) & `W`"); // Stop
-	set_control(m_keys[0], 5, ""); // Reset
-	set_control(m_keys[0], 6, ""); // FrameAdvance
-	set_control(m_keys[0], 7, ""); // StartRecording
-	set_control(m_keys[0], 8, ""); // PlayRecording
-	set_control(m_keys[0], 9, ""); // ExportRecording
-	set_control(m_keys[0], 10, ""); // Readonlymode
-	set_control(m_keys[0], 11, "(`Left Command` | `Right Command`) & `F`"); // ToggleFullscreen
-	set_control(m_keys[0], 12, "(`Left Command` | `Right Command`) & `S`"); // Screenshot
-	set_control(m_keys[0], 13, ""); // Exit
-	set_control(m_keys[0], 14, "(`Left Command` | `Right Command`) & `1`"); // Wiimote1Connect
-	set_control(m_keys[0], 15, "(`Left Command` | `Right Command`) & `2`"); // Wiimote2Connect
-	set_control(m_keys[0], 16, "(`Left Command` | `Right Command`) & `3`"); // Wiimote3Connect
-	set_control(m_keys[0], 17, "(`Left Command` | `Right Command`) & `4`"); // Wiimote4Connect
-	set_control(m_keys[0], 18, "(`Left Command` | `Right Command`) & `5`"); // BalanceBoardConnect
-	set_control(m_keys[0], 19, ""); // VolumeDown
-	set_control(m_keys[0], 20, ""); // VolumeUp
-	set_control(m_keys[0], 21, ""); // VolumeToggleMute
-	set_control(m_keys[0], 22, ""); // ToggleIR
-	set_control(m_keys[0], 23, ""); // ToggleAspectRatio
-	set_control(m_keys[0], 24, ""); // ToggleEFBCopies
-	set_control(m_keys[0], 25, ""); // ToggleFog
-	set_control(m_keys[0], 26, "Tab"); // ToggleThrottle
-	set_control(m_keys[0], 27, ""); // DecreaseFrameLimit
-	set_control(m_keys[0], 28, ""); // IncreaseFrameLimit
-	set_control(m_keys[0], 29, "`1` & !(`Left Command` | `Right Command`)"); // FreelookDecreaseSpeed
-	set_control(m_keys[0], 30, "`2` & !(`Left Command` | `Right Command`)"); // FreelookIncreaseSpeed
-	set_control(m_keys[0], 31, "`F` & !(`Left Command` | `Right Command`)"); // FreelookResetSpeed
-	set_control(m_keys[1], 0, "`E` & !(`Left Command` | `Right Command`)"); // FreelookUp
-	set_control(m_keys[1], 1, "`Q` & !(`Left Command` | `Right Command`)"); // FreelookDown
-	set_control(m_keys[1], 2, "`A` & !(`Left Command` | `Right Command`)"); // FreelookLeft
-	set_control(m_keys[1], 3, "`D` & !(`Left Command` | `Right Command`)"); // FreelookRight
-	set_control(m_keys[1], 4, "`W` & !(`Left Command` | `Right Command`)"); // FreelookZoomIn
-	set_control(m_keys[1], 5, "`S` & !(`Left Command` | `Right Command`)"); // FreelookZoomOut
-	set_control(m_keys[1], 6, "`R` & !(`Left Command` | `Right Command`)"); // FreelookReset
-	set_control(m_keys[1], 7, ""); // DecreaseDepth
-	set_control(m_keys[1], 8, ""); // IncreaseDepth
-	set_control(m_keys[1], 9, ""); // DecreaseConvergence
-	set_control(m_keys[1], 10, ""); // IncreaseConvergence
-	set_control(m_keys[1], 11, "`F1` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot1
-	set_control(m_keys[1], 12, "`F2` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot2
-	set_control(m_keys[1], 13, "`F3` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot3
-	set_control(m_keys[1], 14, "`F4` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot4
-	set_control(m_keys[1], 15, "`F5` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot5
-	set_control(m_keys[1], 16, "`F6` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot6
-	set_control(m_keys[1], 17, "`F7` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot7
-	set_control(m_keys[1], 18, "`F8` & !(`Left Shift` | `Right Shift`)"); // LoadStateSlot8
-	set_control(m_keys[1], 19, ""); // LoadStateSlot9
-	set_control(m_keys[1], 20, ""); // LoadStateSlot10
-	set_control(m_keys[1], 21, "(`Left Shift` | `Right Shift`) & `F1`"); // SaveStateSlot1
-	set_control(m_keys[1], 22, "(`Left Shift` | `Right Shift`) & `F2`"); // SaveStateSlot2
-	set_control(m_keys[1], 23, "(`Left Shift` | `Right Shift`) & `F3`"); // SaveStateSlot3
-	set_control(m_keys[1], 24, "(`Left Shift` | `Right Shift`) & `F4`"); // SaveStateSlot4
-	set_control(m_keys[1], 25, "(`Left Shift` | `Right Shift`) & `F5`"); // SaveStateSlot5
-	set_control(m_keys[1], 26, "(`Left Shift` | `Right Shift`) & `F6`"); // SaveStateSlot6
-	set_control(m_keys[1], 27, "(`Left Shift` | `Right Shift`) & `F7`"); // SaveStateSlot7
-	set_control(m_keys[1], 28, "(`Left Shift` | `Right Shift`) & `F8`"); // SaveStateSlot8
-	set_control(m_keys[1], 29, ""); // SaveStateSlot9
-	set_control(m_keys[1], 30, ""); // SaveStateSlot10
-	set_control(m_keys[1], 31, ""); // SelectStateSlot1
-	set_control(m_keys[2], 0, ""); // SelectStateSlot2
-	set_control(m_keys[2], 1, ""); // SelectStateSlot3
-	set_control(m_keys[2], 2, ""); // SelectStateSlot4
-	set_control(m_keys[2], 3, ""); // SelectStateSlot5
-	set_control(m_keys[2], 4, ""); // SelectStateSlot6
-	set_control(m_keys[2], 5, ""); // SelectStateSlot7
-	set_control(m_keys[2], 6, ""); // SelectStateSlot8
-	set_control(m_keys[2], 7, ""); // SelectStateSlot9
-	set_control(m_keys[2], 8, ""); // SelectStateSlot10
-	set_control(m_keys[2], 9, ""); // SaveSelectedSlot
-	set_control(m_keys[2], 10, ""); // LoadSelectedSlot
-	set_control(m_keys[2], 11, ""); // LoadLastState1
-	set_control(m_keys[2], 12, ""); // LoadLastState2
-	set_control(m_keys[2], 13, ""); // LoadLastState3
-	set_control(m_keys[2], 14, ""); // LoadLastState4
-	set_control(m_keys[2], 15, ""); // LoadLastState5
-	set_control(m_keys[2], 16, ""); // LoadLastState6
-	set_control(m_keys[2], 17, ""); // LoadLastState7
-	set_control(m_keys[2], 18, ""); // LoadLastState8
-	set_control(m_keys[2], 19, ""); // SaveFirstState
-	set_control(m_keys[2], 20, "`F12` & !(`Left Shift` | `Right Shift`)"); // UndoLoadState
-	set_control(m_keys[2], 21, "(`Left Shift` | `Right Shift`) & `F12`"); // UndoSaveState
-	set_control(m_keys[2], 22, ""); // SaveStateFile
-	set_control(m_keys[2], 23, ""); // LoadStateFile
-#else // linux
-	set_control(m_keys[0], 0, "(`Control_L` | `Control_R`) & `O`"); // Open
-	set_control(m_keys[0], 1, ""); // ChangeDisc
-	set_control(m_keys[0], 2, ""); // RefreshList
-	set_control(m_keys[0], 3, "`F10` & !(`Alt_L` | `Alt_R`)"); // PlayPause
-	set_control(m_keys[0], 4, "Escape & !(`Alt_L` | `Alt_R`)"); // Stop
-	set_control(m_keys[0], 5, ""); // Reset
-	set_control(m_keys[0], 6, ""); // FrameAdvance
-	set_control(m_keys[0], 7, ""); // StartRecording
-	set_control(m_keys[0], 8, ""); // PlayRecording
-	set_control(m_keys[0], 9, ""); // ExportRecording
-	set_control(m_keys[0], 10, ""); // Readonlymode
-	set_control(m_keys[0], 11, "(`Alt_L` | `Alt_R`) & Return"); // ToggleFullscreen
-	set_control(m_keys[0], 12, "`F9` & !(`Alt_L` | `Alt_R`)"); // Screenshot
-	set_control(m_keys[0], 13, ""); // Exit
-	set_control(m_keys[0], 14, "(`Alt_L` | `Alt_R`) & `F5`"); // Wiimote1Connect
-	set_control(m_keys[0], 15, "(`Alt_L` | `Alt_R`) & `F6`"); // Wiimote2Connect
-	set_control(m_keys[0], 16, "(`Alt_L` | `Alt_R`) & `F7`"); // Wiimote3Connect
-	set_control(m_keys[0], 17, "(`Alt_L` | `Alt_R`) & `F8`"); // Wiimote4Connect
-	set_control(m_keys[0], 18, "(`Alt_L` | `Alt_R`) & `F9`"); // BalanceBoardConnect
-	set_control(m_keys[0], 19, ""); // VolumeDown
-	set_control(m_keys[0], 20, ""); // VolumeUp
-	set_control(m_keys[0], 21, ""); // VolumeToggleMute
-	set_control(m_keys[0], 22, ""); // ToggleIR
-	set_control(m_keys[0], 23, ""); // ToggleAspectRatio
-	set_control(m_keys[0], 24, ""); // ToggleEFBCopies
-	set_control(m_keys[0], 25, ""); // ToggleFog
-	set_control(m_keys[0], 26, "Tab & !(`Alt_L` | `Alt_R`)"); // ToggleThrottle
-	set_control(m_keys[0], 27, ""); // DecreaseFrameLimit
-	set_control(m_keys[0], 28, ""); // IncreaseFrameLimit
-	set_control(m_keys[0], 29, "1 & !(`Alt_L` | `Alt_R`)"); // FreelookDecreaseSpeed
-	set_control(m_keys[0], 30, "2 & !(`Alt_L` | `Alt_R`)"); // FreelookIncreaseSpeed
-	set_control(m_keys[0], 31, "F & !(`Alt_L` | `Alt_R`)"); // FreelookResetSpeed
-	set_control(m_keys[1], 0, "E & !(`Alt_L` | `Alt_R`)"); // FreelookUp
-	set_control(m_keys[1], 1, "Q & !(`Alt_L` | `Alt_R`)"); // FreelookDown
-	set_control(m_keys[1], 2, "A & !(`Alt_L` | `Alt_R`)"); // FreelookLeft
-	set_control(m_keys[1], 3, "D & !(`Alt_L` | `Alt_R`)"); // FreelookRight
-	set_control(m_keys[1], 4, "W & !(`Alt_L` | `Alt_R`)"); // FreelookZoomIn
-	set_control(m_keys[1], 5, "S & !(`Alt_L` | `Alt_R`)"); // FreelookZoomOut
-	set_control(m_keys[1], 6, "R & !(`Alt_L` | `Alt_R`)"); // FreelookReset
-	set_control(m_keys[1], 7, ""); // DecreaseDepth
-	set_control(m_keys[1], 8, ""); // IncreaseDepth
-	set_control(m_keys[1], 9, ""); // DecreaseConvergence
-	set_control(m_keys[1], 10, ""); // IncreaseConvergence
-	set_control(m_keys[1], 11, "`F1` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot1
-	set_control(m_keys[1], 12, "`F2` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot2
-	set_control(m_keys[1], 13, "`F3` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot3
-	set_control(m_keys[1], 14, "`F4` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot4
-	set_control(m_keys[1], 15, "`F5` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot5
-	set_control(m_keys[1], 16, "`F6` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot6
-	set_control(m_keys[1], 17, "`F7` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot7
-	set_control(m_keys[1], 18, "`F8` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // LoadStateSlot8
-	set_control(m_keys[1], 19, ""); // LoadStateSlot9
-	set_control(m_keys[1], 20, ""); // LoadStateSlot10
-	set_control(m_keys[1], 21, "(`Shift_L` | `Shift_R`) & `F1` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot1
-	set_control(m_keys[1], 22, "(`Shift_L` | `Shift_R`) & `F2` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot2
-	set_control(m_keys[1], 23, "(`Shift_L` | `Shift_R`) & `F3` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot3
-	set_control(m_keys[1], 24, "(`Shift_L` | `Shift_R`) & `F4` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot4
-	set_control(m_keys[1], 25, "(`Shift_L` | `Shift_R`) & `F5` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot5
-	set_control(m_keys[1], 26, "(`Shift_L` | `Shift_R`) & `F6` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot6
-	set_control(m_keys[1], 27, "(`Shift_L` | `Shift_R`) & `F7` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot7
-	set_control(m_keys[1], 28, "(`Shift_L` | `Shift_R`) & `F8` & !(`Alt_L` | `Alt_R`)"); // SaveStateSlot8
-	set_control(m_keys[1], 29, ""); // SaveStateSlot9
-	set_control(m_keys[1], 30, ""); // SaveStateSlot10
-	set_control(m_keys[1], 31, ""); // SelectStateSlot1
-	set_control(m_keys[2], 0, ""); // SelectStateSlot2
-	set_control(m_keys[2], 1, ""); // SelectStateSlot3
-	set_control(m_keys[2], 2, ""); // SelectStateSlot4
-	set_control(m_keys[2], 3, ""); // SelectStateSlot5
-	set_control(m_keys[2], 4, ""); // SelectStateSlot6
-	set_control(m_keys[2], 5, ""); // SelectStateSlot7
-	set_control(m_keys[2], 6, ""); // SelectStateSlot8
-	set_control(m_keys[2], 7, ""); // SelectStateSlot9
-	set_control(m_keys[2], 8, ""); // SelectStateSlot10
-	set_control(m_keys[2], 9, ""); // SaveSelectedSlot
-	set_control(m_keys[2], 10, ""); // LoadSelectedSlot
-	set_control(m_keys[2], 11, ""); // LoadLastState1
-	set_control(m_keys[2], 12, ""); // LoadLastState2
-	set_control(m_keys[2], 13, ""); // LoadLastState3
-	set_control(m_keys[2], 14, ""); // LoadLastState4
-	set_control(m_keys[2], 15, ""); // LoadLastState5
-	set_control(m_keys[2], 16, ""); // LoadLastState6
-	set_control(m_keys[2], 17, ""); // LoadLastState7
-	set_control(m_keys[2], 18, ""); // LoadLastState8
-	set_control(m_keys[2], 19, ""); // SaveFirstState
-	set_control(m_keys[2], 20, "`F12` & !(`Shift_L` | `Shift_R`) & !(`Alt_L` | `Alt_R`)"); // UndoLoadState
-	set_control(m_keys[2], 21, "(`Shift_L` | `Shift_R`) & `F12` & !(`Alt_L` | `Alt_R`)"); // UndoSaveState
-	set_control(m_keys[2], 22, ""); // SaveStateFile
-	set_control(m_keys[2], 23, ""); // LoadStateFile
-#endif
+	for (int set = 0; set < 3; set++)
+	{
+		for (unsigned int key = 0; key < (m_keys[set])->controls.size(); key++)
+		{
+			(m_keys[set])->controls[key]->control_ref->expression = "";
+		}
+	}
 }
diff --git a/Source/Core/Core/HotkeyManager.h b/Source/Core/Core/HotkeyManager.h
index 1e03163def..bd76395046 100644
--- a/Source/Core/Core/HotkeyManager.h
+++ b/Source/Core/Core/HotkeyManager.h
@@ -24,7 +24,7 @@ public:
 	void LoadDefaults(const ControllerInterface& ciface);
 
 private:
-	Buttons* m_keys[6];
+	Buttons* m_keys[3];
 	ControlGroup* m_options;
 };
 
@@ -32,8 +32,13 @@ namespace HotkeyManagerEmu
 {
 	void Initialize(void* const hwnd);
 	void Shutdown();
+	void LoadConfig();
 
 	InputConfig* GetConfig();
-	void GetStatus(u8 _port, HotkeyStatus* _pKeyboardStatus);
+	void GetStatus();
+	bool IsEnabled();
+	void Enable(bool enable_toggle);
 	bool IsPressed(int Id, bool held);
+
+	static bool enabled;
 }
diff --git a/Source/Core/DolphinWX/ControllerConfigDiag.cpp b/Source/Core/DolphinWX/ControllerConfigDiag.cpp
index 909f70b1b1..6f3ae906f5 100644
--- a/Source/Core/DolphinWX/ControllerConfigDiag.cpp
+++ b/Source/Core/DolphinWX/ControllerConfigDiag.cpp
@@ -23,6 +23,7 @@
 #include "Common/SysConf.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
+#include "Core/HotkeyManager.h"
 #include "Core/Movie.h"
 #include "Core/NetPlayProto.h"
 #include "Core/HW/GCKeyboard.h"
@@ -207,12 +208,13 @@ wxStaticBoxSizer* ControllerConfigDiag::CreateWiimoteConfigSizer()
 		wiimote_configure_bt[i]->Bind(wxEVT_BUTTON, &ControllerConfigDiag::ConfigEmulatedWiimote, this);
 
 		// Disable controller type selection for certain circumstances.
-		if (NetPlay::IsNetPlayRunning() || Movie::IsMovieActive())
+		bool wii_game_started = SConfig::GetInstance().m_LocalCoreStartupParameter.bWii || Core::GetState() == Core::CORE_UNINITIALIZED;
+		if (NetPlay::IsNetPlayRunning() || Movie::IsMovieActive() || !wii_game_started)
 			wiimote_source_ch[i]->Disable();
 
 		m_orig_wiimote_sources[i] = g_wiimote_sources[i];
 		wiimote_source_ch[i]->Select(m_orig_wiimote_sources[i]);
-		if (m_orig_wiimote_sources[i] != WIIMOTE_SRC_EMU && m_orig_wiimote_sources[i] != WIIMOTE_SRC_HYBRID)
+		if (!wii_game_started || (m_orig_wiimote_sources[i] != WIIMOTE_SRC_EMU && m_orig_wiimote_sources[i] != WIIMOTE_SRC_HYBRID))
 			wiimote_configure_bt[i]->Disable();
 	}
 
@@ -390,28 +392,13 @@ wxStaticBoxSizer* ControllerConfigDiag::CreateGeneralWiimoteSettingsSizer()
 void ControllerConfigDiag::ConfigEmulatedWiimote(wxCommandEvent& ev)
 {
 	InputConfig* const wiimote_plugin = Wiimote::GetConfig();
-	bool was_init = false;
-	if (g_controller_interface.IsInit()) // check if game is running
-	{
-		was_init = true;
-	}
-	else
-	{
-#if defined(HAVE_X11) && HAVE_X11
-		Window win = X11Utils::XWindowFromHandle(GetHandle());
-		Wiimote::Initialize(reinterpret_cast<void*>(win));
-#else
-		Wiimote::Initialize(reinterpret_cast<void*>(GetHandle()));
-#endif
-	}
+
+	HotkeyManagerEmu::Enable(false);
 
 	InputConfigDialog m_ConfigFrame(this, *wiimote_plugin, _("Dolphin Emulated Wiimote Configuration"), m_wiimote_index_from_conf_bt_id[ev.GetId()]);
 	m_ConfigFrame.ShowModal();
 
-	if (!was_init) // if game isn't running
-	{
-		Wiimote::Shutdown();
-	}
+	HotkeyManagerEmu::Enable(true);
 }
 
 void ControllerConfigDiag::RefreshRealWiimotes(wxCommandEvent&)
@@ -535,24 +522,7 @@ void ControllerConfigDiag::OnGameCubeConfigButton(wxCommandEvent& event)
 	InputConfig* const key_plugin = Keyboard::GetConfig();
 	const int port_num = m_gc_port_config_ids[event.GetId()];
 
-	bool was_init = false;
-
-	// check if game is running
-	if (g_controller_interface.IsInit())
-	{
-		was_init = true;
-	}
-	else
-	{
-#if defined(HAVE_X11) && HAVE_X11
-		Window win = X11Utils::XWindowFromHandle(GetHandle());
-		Pad::Initialize(reinterpret_cast<void*>(win));
-		Keyboard::Initialize(reinterpret_cast<void*>(win));
-#else
-		Pad::Initialize(reinterpret_cast<void*>(GetHandle()));
-		Keyboard::Initialize(reinterpret_cast<void*>(GetHandle()));
-#endif
-	}
+	HotkeyManagerEmu::Enable(false);
 
 	if (SConfig::GetInstance().m_SIDevice[port_num] == SIDEVICE_GC_KEYBOARD)
 	{
@@ -565,10 +535,5 @@ void ControllerConfigDiag::OnGameCubeConfigButton(wxCommandEvent& event)
 		m_ConfigFrame.ShowModal();
 	}
 
-	// if game isn't running
-	if (!was_init)
-	{
-		Keyboard::Shutdown();
-		Pad::Shutdown();
-	}
+	HotkeyManagerEmu::Enable(true);
 }
diff --git a/Source/Core/DolphinWX/Frame.cpp b/Source/Core/DolphinWX/Frame.cpp
index 82a089eb7e..46c2d3538d 100644
--- a/Source/Core/DolphinWX/Frame.cpp
+++ b/Source/Core/DolphinWX/Frame.cpp
@@ -937,7 +937,7 @@ void CFrame::OnGameListCtrl_ItemActivated(wxListEvent& WXUNUSED(event))
 	}
 }
 
-static bool IsHotkey(wxKeyEvent &event, int Id, bool keyUp = false)
+static bool IsHotkey(wxKeyEvent &event, int id, bool held = false)
 {
 	if (Core::GetState() == Core::CORE_UNINITIALIZED)
 		return false;
@@ -945,10 +945,12 @@ static bool IsHotkey(wxKeyEvent &event, int Id, bool keyUp = false)
 	// Input event hotkey
 	if (event.GetKeyCode() == WXK_NONE)
 	{
-		return HotkeyManagerEmu::IsPressed(Id, keyUp);
+		return HotkeyManagerEmu::IsPressed(id, held);
 	}
 
-	return false;
+	return (event.GetKeyCode() != WXK_NONE &&
+		event.GetKeyCode() == SConfig::GetInstance().m_LocalCoreStartupParameter.iHotkey[id] &&
+		event.GetModifiers() == SConfig::GetInstance().m_LocalCoreStartupParameter.iHotkeyModifier[id]);
 }
 
 int GetCmdForHotkey(unsigned int key)
@@ -1263,11 +1265,15 @@ const CGameListCtrl *CFrame::GetGameListCtrl() const
 
 void CFrame::PollHotkeys(wxTimerEvent& event)
 {
+	if (!HotkeyManagerEmu::IsEnabled())
+		return;
+
 	if (Core::GetState() == Core::CORE_UNINITIALIZED || Core::GetState() == Core::CORE_PAUSE)
 		g_controller_interface.UpdateInput();
 
 	if (Core::GetState() != Core::CORE_STOPPING)
 	{
+		HotkeyManagerEmu::GetStatus();
 		wxKeyEvent keyevent = 0;
 
 		if (IsHotkey(keyevent, HK_TOGGLE_THROTTLE))
@@ -1364,24 +1370,26 @@ void CFrame::ParseHotkeys(wxKeyEvent &event)
 	{
 		State::Load(g_saveSlot);
 	}
-	else if (IsHotkey(event, HK_DECREASE_DEPTH))
+	else if (IsHotkey(event, HK_DECREASE_DEPTH, true))
 	{
 		if (--g_Config.iStereoDepth < 0)
 			g_Config.iStereoDepth = 0;
 	}
-	else if (IsHotkey(event, HK_INCREASE_DEPTH))
+	else if (IsHotkey(event, HK_INCREASE_DEPTH, true))
 	{
 		if (++g_Config.iStereoDepth > 100)
 			g_Config.iStereoDepth = 100;
 	}
-	else if (IsHotkey(event, HK_DECREASE_CONVERGENCE))
+	else if (IsHotkey(event, HK_DECREASE_CONVERGENCE, true))
 	{
-		if (--g_Config.iStereoConvergence < 0)
+		g_Config.iStereoConvergence -= 5;
+		if (g_Config.iStereoConvergence < 0)
 			g_Config.iStereoConvergence = 0;
 	}
-	else if (IsHotkey(event, HK_INCREASE_CONVERGENCE))
+	else if (IsHotkey(event, HK_INCREASE_CONVERGENCE, true))
 	{
-		if (++g_Config.iStereoConvergence > 500)
+		g_Config.iStereoConvergence += 5;
+		if (g_Config.iStereoConvergence > 500)
 			g_Config.iStereoConvergence = 500;
 	}
 
@@ -1398,25 +1406,26 @@ void CFrame::ParseHotkeys(wxKeyEvent &event)
 		}
 
 		unsigned int i = NUM_HOTKEYS;
-		if (!SConfig::GetInstance().m_LocalCoreStartupParameter.bRenderToMain || TASInputHasFocus())
+		for (i = 0; i < NUM_HOTKEYS; i++)
 		{
-			for (i = 0; i < NUM_HOTKEYS; i++)
+			bool held = false;
+			if (i == HK_FRAME_ADVANCE)
+				held = true;
+
+			if (IsHotkey(event, i, held))
 			{
-				if (IsHotkey(event, i))
+				int cmd = GetCmdForHotkey(i);
+				if (cmd >= 0)
 				{
-					int cmd = GetCmdForHotkey(i);
-					if (cmd >= 0)
+					wxCommandEvent evt(wxEVT_MENU, cmd);
+					wxMenuItem* item = GetMenuBar()->FindItem(cmd);
+					if (item && item->IsCheckable())
 					{
-						wxCommandEvent evt(wxEVT_MENU, cmd);
-						wxMenuItem *item = GetMenuBar()->FindItem(cmd);
-						if (item && item->IsCheckable())
-						{
-							item->wxMenuItemBase::Toggle();
-							evt.SetInt(item->IsChecked());
-						}
-						GetEventHandler()->AddPendingEvent(evt);
-						break;
+						item->wxMenuItemBase::Toggle();
+						evt.SetInt(item->IsChecked());
 					}
+					GetEventHandler()->AddPendingEvent(evt);
+					break;
 				}
 			}
 		}
@@ -1436,37 +1445,34 @@ void CFrame::ParseHotkeys(wxKeyEvent &event)
 	// Actually perform the Wiimote connection or disconnection
 	if (Core::GetState() != Core::CORE_UNINITIALIZED)
 	{
-		if (WiimoteId >= 0)
+		if (WiimoteId >= 0 && SConfig::GetInstance().m_LocalCoreStartupParameter.bWii)
 		{
 			wxCommandEvent evt;
 			evt.SetId(IDM_CONNECT_WIIMOTE1 + WiimoteId);
 			OnConnectWiimote(evt);
 		}
 
-		if (g_Config.bFreeLook)
-		{
-			static float debugSpeed = 1.0f;
+		static float debugSpeed = 1.0f;
 
-			if (IsHotkey(event, HK_FREELOOK_DECREASE_SPEED))
-				debugSpeed /= 2.0f;
-			else if (IsHotkey(event, HK_FREELOOK_INCREASE_SPEED))
-				debugSpeed *= 2.0f;
-			else if (IsHotkey(event, HK_FREELOOK_RESET_SPEED))
-				debugSpeed = 1.0f;
-			else if (IsHotkey(event, HK_FREELOOK_UP))
-				VertexShaderManager::TranslateView(0.0f, 0.0f, -debugSpeed);
-			else if (IsHotkey(event, HK_FREELOOK_DOWN))
-				VertexShaderManager::TranslateView(0.0f, 0.0f, debugSpeed);
-			else if (IsHotkey(event, HK_FREELOOK_LEFT))
-				VertexShaderManager::TranslateView(debugSpeed, 0.0f);
-			else if (IsHotkey(event, HK_FREELOOK_RIGHT))
-				VertexShaderManager::TranslateView(-debugSpeed, 0.0f);
-			else if (IsHotkey(event, HK_FREELOOK_ZOOM_IN))
-				VertexShaderManager::TranslateView(0.0f, debugSpeed);
-			else if (IsHotkey(event, HK_FREELOOK_ZOOM_OUT))
-				VertexShaderManager::TranslateView(0.0f, -debugSpeed);
-			else if (IsHotkey(event, HK_FREELOOK_RESET))
-				VertexShaderManager::ResetView();
-		}
+		if (IsHotkey(event, HK_FREELOOK_DECREASE_SPEED, true))
+			debugSpeed /= 1.1f;
+		else if (IsHotkey(event, HK_FREELOOK_INCREASE_SPEED, true))
+			debugSpeed *= 1.1f;
+		else if (IsHotkey(event, HK_FREELOOK_RESET_SPEED, true))
+			debugSpeed = 1.0f;
+		else if (IsHotkey(event, HK_FREELOOK_UP, true))
+			VertexShaderManager::TranslateView(0.0f, 0.0f, -debugSpeed);
+		else if (IsHotkey(event, HK_FREELOOK_DOWN, true))
+			VertexShaderManager::TranslateView(0.0f, 0.0f, debugSpeed);
+		else if (IsHotkey(event, HK_FREELOOK_LEFT, true))
+			VertexShaderManager::TranslateView(debugSpeed, 0.0f);
+		else if (IsHotkey(event, HK_FREELOOK_RIGHT, true))
+			VertexShaderManager::TranslateView(-debugSpeed, 0.0f);
+		else if (IsHotkey(event, HK_FREELOOK_ZOOM_IN, true))
+			VertexShaderManager::TranslateView(0.0f, debugSpeed);
+		else if (IsHotkey(event, HK_FREELOOK_ZOOM_OUT, true))
+			VertexShaderManager::TranslateView(0.0f, -debugSpeed);
+		else if (IsHotkey(event, HK_FREELOOK_RESET, true))
+			VertexShaderManager::ResetView();
 	}
 }
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index 5ae3e62076..fda4f4ee0e 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -51,6 +51,7 @@
 #include "Core/State.h"
 #include "Core/HW/CPU.h"
 #include "Core/HW/DVDInterface.h"
+#include "Core/HW/GCKeyboard.h"
 #include "Core/HW/GCPad.h"
 #include "Core/HW/ProcessorInterface.h"
 #include "Core/HW/SI_Device.h"
@@ -238,8 +239,8 @@ wxMenuBar* CFrame::CreateMenu()
 	pOptionsMenu->Append(IDM_CONFIG_GFX_BACKEND, _("&Graphics Settings"));
 	pOptionsMenu->Append(IDM_CONFIG_AUDIO, _("&Audio Settings"));
 	pOptionsMenu->Append(IDM_CONFIG_CONTROLLERS, _("&Controller Settings"));
+	pOptionsMenu->Append(IDM_CONFIG_MENU_COMMANDS, _("&Key Shortcuts"));
 	pOptionsMenu->Append(IDM_CONFIG_HOTKEYS, _("&Hotkey Settings"));
-	pOptionsMenu->Append(IDM_CONFIG_MENU_COMMANDS, _("&Menu Accelerators"));
 	if (g_pCodeWindow)
 	{
 		pOptionsMenu->AppendSeparator();
@@ -686,7 +687,8 @@ void CFrame::BootGame(const std::string& filename)
 // Open file to boot
 void CFrame::OnOpen(wxCommandEvent& WXUNUSED (event))
 {
-	DoOpen(true);
+	if (Core::GetState() == Core::CORE_UNINITIALIZED)
+		DoOpen(true);
 }
 
 void CFrame::DoOpen(bool Boot)
@@ -1365,27 +1367,31 @@ void CFrame::OnConfigHotkey(wxCommandEvent& WXUNUSED (event))
 	InputConfig* const hotkey_plugin = HotkeyManagerEmu::GetConfig();
 
 	// check if game is running
-	if (g_controller_interface.IsInit())
+	bool game_running = false;
+	if (Core::GetState() == Core::CORE_RUN)
 	{
-		was_init = true;
-	}
-	else
-	{
-#if defined(HAVE_X11) && HAVE_X11
-		Window win = X11Utils::XWindowFromHandle(GetHandle());
-		HotkeyManagerEmu::Initialize(reinterpret_cast<void*>(win));
-#else
-		HotkeyManagerEmu::Initialize(reinterpret_cast<void*>(GetHandle()));
-#endif
+		Core::SetState(Core::CORE_PAUSE);
+		game_running = true;
 	}
 
+	HotkeyManagerEmu::Enable(false);
+
 	InputConfigDialog m_ConfigFrame(this, *hotkey_plugin, _("Dolphin Hotkeys"));
 	m_ConfigFrame.ShowModal();
 
+	// Update references in case controllers were refreshed
+	if (SConfig::GetInstance().m_LocalCoreStartupParameter.bWii)
+		Wiimote::LoadConfig();
+	Keyboard::LoadConfig();
+	Pad::LoadConfig();
+	HotkeyManagerEmu::LoadConfig();
+
+	HotkeyManagerEmu::Enable(true);
+
 	// if game isn't running
-	if (!was_init)
+	if (game_running)
 	{
-		HotkeyManagerEmu::Shutdown();
+		Core::SetState(Core::CORE_RUN);
 	}
 
 	// Update the GUI in case menu accelerators were changed
@@ -1761,7 +1767,7 @@ void CFrame::UpdateGUI()
 	GetMenuBar()->FindItem(IDM_SCREENSHOT)->Enable(Running || Paused);
 	GetMenuBar()->FindItem(IDM_TOGGLE_FULLSCREEN)->Enable(Running || Paused);
 
-	// Update Menu Accelerators
+	// Update Key Shortcuts
 	for (unsigned int i = 0; i < NUM_HOTKEYS; i++)
 	{
 		if (GetCmdForHotkey(i) == -1)
diff --git a/Source/Core/DolphinWX/HotkeyDlg.h b/Source/Core/DolphinWX/HotkeyDlg.h
index db4c687c52..9dd5307928 100644
--- a/Source/Core/DolphinWX/HotkeyDlg.h
+++ b/Source/Core/DolphinWX/HotkeyDlg.h
@@ -29,7 +29,7 @@ class HotkeyConfigDialog : public wxDialog
 public:
 	HotkeyConfigDialog(wxWindow* parent,
 			wxWindowID id = wxID_ANY,
-			const wxString &title = _("Menu Accelerators"),
+			const wxString &title = _("Key Shortcuts"),
 			const wxPoint& pos = wxDefaultPosition,
 			const wxSize& size = wxDefaultSize,
 			long style = wxDEFAULT_DIALOG_STYLE);
diff --git a/Source/Core/DolphinWX/InputConfigDiag.cpp b/Source/Core/DolphinWX/InputConfigDiag.cpp
index 653f92ea11..d45458535a 100644
--- a/Source/Core/DolphinWX/InputConfigDiag.cpp
+++ b/Source/Core/DolphinWX/InputConfigDiag.cpp
@@ -44,6 +44,10 @@
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
 #include "Common/MsgHandler.h"
+#include "Core/Core.h"
+#include "Core/HotkeyManager.h"
+#include "Core/HW/GCKeyboard.h"
+#include "Core/HW/GCPad.h"
 #include "Core/HW/Wiimote.h"
 #include "DolphinWX/InputConfigDiag.h"
 #include "DolphinWX/WxUtils.h"
@@ -740,6 +744,8 @@ void InputConfigDialog::UpdateDeviceComboBox()
 
 void GamepadPage::RefreshDevices(wxCommandEvent&)
 {
+	bool was_unpaused = Core::PauseAndLock(true);
+
 	std::lock_guard<std::recursive_mutex> lk(m_config.controls_lock);
 
 	// refresh devices
@@ -750,6 +756,14 @@ void GamepadPage::RefreshDevices(wxCommandEvent&)
 
 	// update device cbox
 	m_config_dialog->UpdateDeviceComboBox();
+
+	//if (SConfig::GetInstance().m_LocalCoreStartupParameter.bWii)
+	Wiimote::LoadConfig();
+	Keyboard::LoadConfig();
+	Pad::LoadConfig();
+	HotkeyManagerEmu::LoadConfig();
+
+	Core::PauseAndLock(false, was_unpaused);
 }
 
 ControlGroupBox::~ControlGroupBox()
diff --git a/Source/Core/InputCommon/ControllerInterface/ControllerInterface.cpp b/Source/Core/InputCommon/ControllerInterface/ControllerInterface.cpp
index 3eb1b95ff2..1330cb1e0a 100644
--- a/Source/Core/InputCommon/ControllerInterface/ControllerInterface.cpp
+++ b/Source/Core/InputCommon/ControllerInterface/ControllerInterface.cpp
@@ -136,9 +136,6 @@ void ControllerInterface::UpdateInput()
 {
 	std::unique_lock<std::recursive_mutex> lk(update_lock, std::defer_lock);
 
-	if (!lk.try_lock())
-		return;
-
 	for (ciface::Core::Device* d : m_devices)
 		d->UpdateInput();
 }
diff --git a/Source/Core/InputCommon/InputConfig.cpp b/Source/Core/InputCommon/InputConfig.cpp
index da5bb5081a..ef517d407d 100644
--- a/Source/Core/InputCommon/InputConfig.cpp
+++ b/Source/Core/InputCommon/InputConfig.cpp
@@ -7,13 +7,6 @@
 #include "Core/HW/Wiimote.h"
 #include "InputCommon/InputConfig.h"
 
-InputConfig::~InputConfig()
-{
-	// delete pads
-	for (ControllerEmu* pad : controllers)
-		delete pad;
-}
-
 bool InputConfig::LoadConfig(bool isGC)
 {
 	IniFile inifile;
diff --git a/Source/Core/InputCommon/InputConfig.h b/Source/Core/InputCommon/InputConfig.h
index e6e80c83fc..a234cdf167 100644
--- a/Source/Core/InputCommon/InputConfig.h
+++ b/Source/Core/InputCommon/InputConfig.h
@@ -21,8 +21,6 @@ public:
 		const char* const _profile_name)
 		: ini_name(_ini_name), gui_name(_gui_name), profile_name(_profile_name) {}
 
-	~InputConfig();
-
 	bool LoadConfig(bool isGC);
 	void SaveConfig();