diff --git a/Source/Core/DolphinWX/Debugger/CodeWindow.cpp b/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
index c1e10e248e..4f14da7302 100644
--- a/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
+++ b/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
@@ -123,6 +123,8 @@ CCodeWindow::CCodeWindow(CFrame* parent, wxWindowID id, const wxPoint& position,
   Bind(wxEVT_MENU, &CCodeWindow::OnJitMenu, this, IDM_CLEAR_CODE_CACHE, IDM_SEARCH_INSTRUCTION);
   Bind(wxEVT_MENU, &CCodeWindow::OnSymbolsMenu, this, IDM_CLEAR_SYMBOLS, IDM_PATCH_HLE_FUNCTIONS);
   Bind(wxEVT_MENU, &CCodeWindow::OnProfilerMenu, this, IDM_PROFILE_BLOCKS, IDM_WRITE_PROFILE);
+  Bind(wxEVT_MENU, &CCodeWindow::OnBootToPauseSelected, this, IDM_BOOT_TO_PAUSE);
+  Bind(wxEVT_MENU, &CCodeWindow::OnAutomaticStartSelected, this, IDM_AUTOMATIC_START);
 
   // Toolbar
   Bind(wxEVT_MENU, &CCodeWindow::OnCodeStep, this, IDM_STEP, IDM_GOTOPC);
@@ -478,54 +480,50 @@ void CCodeWindow::UpdateCallstack()
 // CPU Mode and JIT Menu
 void CCodeWindow::OnCPUMode(wxCommandEvent& event)
 {
-  switch (event.GetId())
-  {
-  case IDM_INTERPRETER:
-    PowerPC::SetMode(event.IsChecked() ? PowerPC::CoreMode::Interpreter : PowerPC::CoreMode::JIT);
-    break;
-  case IDM_BOOT_TO_PAUSE:
-    SConfig::GetInstance().bBootToPause = event.IsChecked();
-    return;
-  case IDM_AUTOMATIC_START:
-    SConfig::GetInstance().bAutomaticStart = event.IsChecked();
-    return;
-  case IDM_JIT_OFF:
-    SConfig::GetInstance().bJITOff = event.IsChecked();
-    break;
-  case IDM_JIT_LS_OFF:
-    SConfig::GetInstance().bJITLoadStoreOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLXZ_OFF:
-    SConfig::GetInstance().bJITLoadStorelXzOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLWZ_OFF:
-    SConfig::GetInstance().bJITLoadStorelwzOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLBZX_OFF:
-    SConfig::GetInstance().bJITLoadStorelbzxOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSF_OFF:
-    SConfig::GetInstance().bJITLoadStoreFloatingOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSP_OFF:
-    SConfig::GetInstance().bJITLoadStorePairedOff = event.IsChecked();
-    break;
-  case IDM_JIT_FP_OFF:
-    SConfig::GetInstance().bJITFloatingPointOff = event.IsChecked();
-    break;
-  case IDM_JIT_I_OFF:
-    SConfig::GetInstance().bJITIntegerOff = event.IsChecked();
-    break;
-  case IDM_JIT_P_OFF:
-    SConfig::GetInstance().bJITPairedOff = event.IsChecked();
-    break;
-  case IDM_JIT_SR_OFF:
-    SConfig::GetInstance().bJITSystemRegistersOff = event.IsChecked();
-    break;
-  }
+  Core::RunAsCPUThread([&event] {
+    switch (event.GetId())
+    {
+    case IDM_INTERPRETER:
+      PowerPC::SetMode(event.IsChecked() ? PowerPC::CoreMode::Interpreter : PowerPC::CoreMode::JIT);
+      break;
+    case IDM_JIT_OFF:
+      SConfig::GetInstance().bJITOff = event.IsChecked();
+      break;
+    case IDM_JIT_LS_OFF:
+      SConfig::GetInstance().bJITLoadStoreOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLXZ_OFF:
+      SConfig::GetInstance().bJITLoadStorelXzOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLWZ_OFF:
+      SConfig::GetInstance().bJITLoadStorelwzOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLBZX_OFF:
+      SConfig::GetInstance().bJITLoadStorelbzxOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSF_OFF:
+      SConfig::GetInstance().bJITLoadStoreFloatingOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSP_OFF:
+      SConfig::GetInstance().bJITLoadStorePairedOff = event.IsChecked();
+      break;
+    case IDM_JIT_FP_OFF:
+      SConfig::GetInstance().bJITFloatingPointOff = event.IsChecked();
+      break;
+    case IDM_JIT_I_OFF:
+      SConfig::GetInstance().bJITIntegerOff = event.IsChecked();
+      break;
+    case IDM_JIT_P_OFF:
+      SConfig::GetInstance().bJITPairedOff = event.IsChecked();
+      break;
+    case IDM_JIT_SR_OFF:
+      SConfig::GetInstance().bJITSystemRegistersOff = event.IsChecked();
+      break;
+    }
 
-  // Clear the JIT cache to enable these changes
-  JitInterface::ClearCache();
+    // Clear the JIT cache to enable these changes
+    JitInterface::ClearCache();
+  });
 }
 
 void CCodeWindow::OnJitMenu(wxCommandEvent& event)
@@ -537,7 +535,7 @@ void CCodeWindow::OnJitMenu(wxCommandEvent& event)
     break;
 
   case IDM_CLEAR_CODE_CACHE:
-    JitInterface::ClearCache();
+    Core::RunAsCPUThread(JitInterface::ClearCache);
     break;
 
   case IDM_SEARCH_INSTRUCTION:
diff --git a/Source/Core/DolphinWX/Debugger/CodeWindow.h b/Source/Core/DolphinWX/Debugger/CodeWindow.h
index 76024eb1d4..8a43ebcedf 100644
--- a/Source/Core/DolphinWX/Debugger/CodeWindow.h
+++ b/Source/Core/DolphinWX/Debugger/CodeWindow.h
@@ -133,6 +133,9 @@ private:
   void OnJitMenu(wxCommandEvent& event);
   void OnProfilerMenu(wxCommandEvent& event);
 
+  void OnBootToPauseSelected(wxCommandEvent& event);
+  void OnAutomaticStartSelected(wxCommandEvent& event);
+
   void OnSymbolListChange(wxCommandEvent& event);
   void OnCallstackListChange(wxCommandEvent& event);
   void OnCallersListChange(wxCommandEvent& event);
diff --git a/Source/Core/DolphinWX/Debugger/CodeWindowFunctions.cpp b/Source/Core/DolphinWX/Debugger/CodeWindowFunctions.cpp
index 7bc7f07210..7214ec26b9 100644
--- a/Source/Core/DolphinWX/Debugger/CodeWindowFunctions.cpp
+++ b/Source/Core/DolphinWX/Debugger/CodeWindowFunctions.cpp
@@ -505,6 +505,16 @@ void CCodeWindow::OnChangeFont(wxCommandEvent& event)
   // TODO: Send event to all panels that tells them to reload the font when it changes.
 }
 
+void CCodeWindow::OnBootToPauseSelected(wxCommandEvent& event)
+{
+  SConfig::GetInstance().bBootToPause = event.IsChecked();
+}
+
+void CCodeWindow::OnAutomaticStartSelected(wxCommandEvent& event)
+{
+  SConfig::GetInstance().bAutomaticStart = event.IsChecked();
+}
+
 // Toggle windows
 
 wxPanel* CCodeWindow::GetUntypedPanel(int id) const
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index 3905c75984..787f5ae1c1 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -237,18 +237,18 @@ void CFrame::BindDebuggerMenuBarUpdateEvents()
 
   Bind(wxEVT_UPDATE_UI, &CFrame::OnUpdateInterpreterMenuItem, this, IDM_INTERPRETER);
 
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LS_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLXZ_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLWZ_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLBZX_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSF_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSP_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_FP_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_I_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_P_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_SR_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_CLEAR_CODE_CACHE);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LS_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLXZ_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLWZ_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLBZX_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSF_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSP_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_FP_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_I_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_P_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_SR_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_CLEAR_CODE_CACHE);
 
   Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreInitialized, IDM_SEARCH_INSTRUCTION);
   Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreInitialized, IDM_CLEAR_SYMBOLS);
@@ -1111,7 +1111,7 @@ void CFrame::OnRescanGameList(wxCommandEvent& WXUNUSED(event))
 
 void CFrame::OnUpdateInterpreterMenuItem(wxUpdateUIEvent& event)
 {
-  WxEventUtils::OnEnableIfCorePaused(event);
+  WxEventUtils::OnEnableIfCoreRunning(event);
 
   if (GetMenuBar()->FindItem(IDM_INTERPRETER)->IsChecked())
     return;
diff --git a/Source/Core/DolphinWX/Globals.h b/Source/Core/DolphinWX/Globals.h
index 0ade18f159..d85d5add8e 100644
--- a/Source/Core/DolphinWX/Globals.h
+++ b/Source/Core/DolphinWX/Globals.h
@@ -208,8 +208,6 @@ enum
   // --------------------
   // CPU Mode
   IDM_INTERPRETER,
-  IDM_AUTOMATIC_START,
-  IDM_BOOT_TO_PAUSE,
   IDM_JIT_NO_BLOCK_CACHE,
   IDM_JIT_NO_BLOCK_LINKING,  // JIT
   IDM_JIT_OFF,
@@ -223,7 +221,10 @@ enum
   IDM_JIT_FP_OFF,
   IDM_JIT_P_OFF,
   IDM_JIT_SR_OFF,
+
   IDM_FONT_PICKER,
+  IDM_AUTOMATIC_START,
+  IDM_BOOT_TO_PAUSE,
 
   // Symbols
   IDM_CLEAR_SYMBOLS,