diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 113ac0e553..c3bbaa4515 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -267,6 +267,8 @@ void Stop()  // - Hammertime!
 
 		g_video_backend->Video_ExitLoop();
 	}
+	if (s_emu_thread.joinable())
+		s_emu_thread.join();
 }
 
 static void DeclareAsCPUThread()
@@ -793,12 +795,6 @@ void UpdateTitle()
 	Host_UpdateTitle(SMessage);
 }
 
-void Shutdown()
-{
-	if (s_emu_thread.joinable())
-		s_emu_thread.join();
-}
-
 void SetOnStoppedCallback(StoppedCallbackFunc callback)
 {
 	s_on_stopped_callback = callback;
diff --git a/Source/Core/Core/Core.h b/Source/Core/Core/Core.h
index 341036bead..63eabe247b 100644
--- a/Source/Core/Core/Core.h
+++ b/Source/Core/Core/Core.h
@@ -40,7 +40,6 @@ enum EState
 
 bool Init();
 void Stop();
-void Shutdown();
 
 std::string StopMessage(bool, std::string);
 
diff --git a/Source/Core/Core/CoreTiming.cpp b/Source/Core/Core/CoreTiming.cpp
index d9872dcc3b..041c3b150e 100644
--- a/Source/Core/Core/CoreTiming.cpp
+++ b/Source/Core/Core/CoreTiming.cpp
@@ -224,8 +224,7 @@ u64 GetIdleTicks()
 // schedule things to be executed on the main thread.
 void ScheduleEvent_Threadsafe(int cyclesIntoFuture, int event_type, u64 userdata)
 {
-	// TODO: Fix UI thread safety problems, and enable this assertion
-	// _assert_msg_(POWERPC, !Core::IsCPUThread(), "ScheduleEvent_Threadsafe from wrong thread");
+	_assert_msg_(POWERPC, !Core::IsCPUThread(), "ScheduleEvent_Threadsafe from wrong thread");
 	std::lock_guard<std::mutex> lk(tsWriteLock);
 	Event ne;
 	ne.time = globalTimer + cyclesIntoFuture;
@@ -287,8 +286,8 @@ static void AddEventToQueue(Event* ne)
 // than Advance
 void ScheduleEvent(int cyclesIntoFuture, int event_type, u64 userdata)
 {
-	// TODO: Fix UI thread safety problems, and enable this assertion
-	//_assert_msg_(POWERPC, Core::IsCPUThread(), "ScheduleEvent from wrong thread");
+	_assert_msg_(POWERPC, Core::IsCPUThread() || Core::GetState() == Core::CORE_PAUSE,
+				 "ScheduleEvent from wrong thread");
 	Event *ne = GetNewEvent();
 	ne->userdata = userdata;
 	ne->type = event_type;
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index de41814259..4edb08980f 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -1584,17 +1584,21 @@ void CFrame::ConnectWiimote(int wm_idx, bool connect)
 {
 	if (Core::IsRunning() && SConfig::GetInstance().m_LocalCoreStartupParameter.bWii)
 	{
+		bool was_unpaused = Core::PauseAndLock(true);
 		GetUsbPointer()->AccessWiiMote(wm_idx | 0x100)->Activate(connect);
 		wxString msg(wxString::Format(_("Wiimote %i %s"), wm_idx + 1,
 					connect ? _("Connected") : _("Disconnected")));
 		Core::DisplayMessage(WxStrToStr(msg), 3000);
 		Host_UpdateMainFrame();
+		Core::PauseAndLock(false, was_unpaused);
 	}
 }
 
 void CFrame::OnConnectWiimote(wxCommandEvent& event)
 {
+	bool was_unpaused = Core::PauseAndLock(true);
 	ConnectWiimote(event.GetId() - IDM_CONNECT_WIIMOTE1, !GetUsbPointer()->AccessWiiMote((event.GetId() - IDM_CONNECT_WIIMOTE1) | 0x100)->IsConnected());
+	Core::PauseAndLock(false, was_unpaused);
 }
 
 // Toggle fullscreen. In Windows the fullscreen mode is accomplished by expanding the m_Panel to cover
@@ -1792,6 +1796,7 @@ void CFrame::UpdateGUI()
 	GetMenuBar()->FindItem(IDM_CONNECT_BALANCEBOARD)->Enable(RunningWii);
 	if (RunningWii)
 	{
+		bool was_unpaused = Core::PauseAndLock(true);
 		GetMenuBar()->FindItem(IDM_CONNECT_WIIMOTE1)->Check(GetUsbPointer()->
 				AccessWiiMote(0x0100)->IsConnected());
 		GetMenuBar()->FindItem(IDM_CONNECT_WIIMOTE2)->Check(GetUsbPointer()->
@@ -1802,6 +1807,7 @@ void CFrame::UpdateGUI()
 				AccessWiiMote(0x0103)->IsConnected());
 		GetMenuBar()->FindItem(IDM_CONNECT_BALANCEBOARD)->Check(GetUsbPointer()->
 				AccessWiiMote(0x0104)->IsConnected());
+		Core::PauseAndLock(false, was_unpaused);
 	}
 
 	if (m_ToolBar)
diff --git a/Source/Core/DolphinWX/Main.cpp b/Source/Core/DolphinWX/Main.cpp
index 8734eebedf..300d03720b 100644
--- a/Source/Core/DolphinWX/Main.cpp
+++ b/Source/Core/DolphinWX/Main.cpp
@@ -371,7 +371,6 @@ void DolphinApp::OnEndSession(wxCloseEvent& event)
 
 int DolphinApp::OnExit()
 {
-	Core::Shutdown();
 	UICommon::Shutdown();
 
 	delete m_locale;
diff --git a/Source/Core/DolphinWX/MainNoGUI.cpp b/Source/Core/DolphinWX/MainNoGUI.cpp
index fffdbb3a4a..bcb9893f33 100644
--- a/Source/Core/DolphinWX/MainNoGUI.cpp
+++ b/Source/Core/DolphinWX/MainNoGUI.cpp
@@ -348,7 +348,6 @@ int main(int argc, char* argv[])
 	while (PowerPC::GetState() != PowerPC::CPU_POWERDOWN)
 		updateMainFrameEvent.Wait();
 
-	Core::Shutdown();
 	platform->Shutdown();
 	UICommon::Shutdown();