diff --git a/Source/Core/Core/Src/Core.cpp b/Source/Core/Core/Src/Core.cpp
index 7d36529f77..4e48bde02e 100644
--- a/Source/Core/Core/Src/Core.cpp
+++ b/Source/Core/Core/Src/Core.cpp
@@ -213,19 +213,15 @@ void Stop()  // - Hammertime!
 	PowerPC::Stop();
 	CCPU::StepOpcode();  // Kick it if it's waiting (code stepping wait loop)
 
-	// Wait until the CPU finishes exiting the main run loop
-	cpuRunloopQuit.Wait();
-	cpuRunloopQuit.Shutdown();
-	// At this point, we must be out of the CPU:s runloop.
-
-	// Stop audio thread.
-	CPluginManager::GetInstance().GetDSP()->DSP_StopSoundStream();
- 
 	// If dual core mode, the CPU thread should immediately exit here.
 	if (_CoreParameter.bCPUThread) {
 		NOTICE_LOG(CONSOLE, "%s", StopMessage(true, "Wait for Video Loop to exit ...").c_str());
 		CPluginManager::GetInstance().GetVideo()->Video_ExitLoop();
 	}
+	// Wait until the CPU finishes exiting the main run loop
+	cpuRunloopQuit.Wait();
+	cpuRunloopQuit.Shutdown();
+	// At this point, we must be out of the CPU:s runloop.
 
 	// Video_EnterLoop() should now exit so that EmuThread() will continue concurrently with the rest
 	// of the commands in this function. We no longer rely on Postmessage. 
@@ -296,7 +292,6 @@ THREAD_RETURN CpuThread(void *pArg)
  
 	// Enter CPU run loop. When we leave it - we are done.
 	CCPU::Run();
-	cpuRunloopQuit.Set();
 
  	return 0;
 }
@@ -369,30 +364,13 @@ THREAD_RETURN EmuThread(void *pArg)
 	dspInit.bOnThread				= _CoreParameter.bDSPThread;
 
 	Plugins.GetDSP()->Initialize((void *)&dspInit);
-
-	// Load and Init PadPlugin
-	for (int i = 0; i < MAXPADS; i++)
-	{			
-		SPADInitialize PADInitialize;
-		PADInitialize.hWnd		= g_pWindowHandle;
-		PADInitialize.pLog		= Callback_PADLog;
-		PADInitialize.padNumber	= i;
-		// This is may be needed to avoid a SDL problem
-		//Plugins.FreeWiimote();
-		// Check if we should init the plugin
-		if (Plugins.OkayToInitPlugin(i))
-		{
-			Plugins.GetPad(i)->Initialize(&PADInitialize);
-
-			// Check if joypad open failed, in that case try again
-			if (PADInitialize.padNumber == -1)
-			{
-				Plugins.GetPad(i)->Shutdown();
-				Plugins.FreePad(i);
-				Plugins.GetPad(i)->Initialize(&PADInitialize);
-			}
-		}
-	}
+	
+	SPADInitialize PADInitialize;
+	PADInitialize.hWnd		= g_pWindowHandle;
+	PADInitialize.pLog		= Callback_PADLog;
+	// This is may be needed to avoid a SDL problem
+	//Plugins.FreeWiimote();
+	Plugins.GetPad(0)->Initialize(&PADInitialize);
 
 	// Load and Init WiimotePlugin - only if we are booting in wii mode	
 	if (_CoreParameter.bWii)
@@ -459,7 +437,6 @@ THREAD_RETURN EmuThread(void *pArg)
 		// then we lose the powerdown check. ... unless powerdown sends a message :P
 		while (PowerPC::GetState() != PowerPC::CPU_POWERDOWN)
 		{
-			Host_UpdateMainFrame();
 			if (Callback_PeekMessages)
 				Callback_PeekMessages();
 			Common::SleepCurrentThread(20);
@@ -507,6 +484,8 @@ THREAD_RETURN EmuThread(void *pArg)
 	// We have now exited the Video Loop and will shut down
 
 	g_bHwInit = false;
+	// Stop audio thread.
+	Plugins.GetDSP()->DSP_StopSoundStream();
 
 	WARN_LOG(CONSOLE, "%s", StopMessage(false, "Shutting down plugins").c_str());
 	Plugins.ShutdownVideoPlugin();
@@ -521,8 +500,7 @@ THREAD_RETURN EmuThread(void *pArg)
 	NOTICE_LOG(CONSOLE, "Stop [Main Thread]\t\t---- Shutdown complete ----");
 
 	g_bStopping = false;
-
-	Host_UpdateMainFrame();
+	cpuRunloopQuit.Set();
 
 	return 0;
 }
diff --git a/Source/Core/Core/Src/CoreParameter.h b/Source/Core/Core/Src/CoreParameter.h
index 28ae9bd131..c3079a8835 100644
--- a/Source/Core/Core/Src/CoreParameter.h
+++ b/Source/Core/Core/Src/CoreParameter.h
@@ -25,7 +25,7 @@
 #include "IniFile.h"
 #include <string>
 
-#define MAXPADS 4
+#define MAXPADS 1
 #define MAXWIIMOTES 1
 
 struct SCoreStartupParameter
diff --git a/Source/Core/Core/Src/HW/SI_DeviceAMBaseboard.cpp b/Source/Core/Core/Src/HW/SI_DeviceAMBaseboard.cpp
index 3af82f4c23..79b40d7bdc 100644
--- a/Source/Core/Core/Src/HW/SI_DeviceAMBaseboard.cpp
+++ b/Source/Core/Core/Src/HW/SI_DeviceAMBaseboard.cpp
@@ -144,7 +144,7 @@ int CSIDevice_AMBaseboard::RunBuffer(u8* _pBuffer, int _iLength)
 							DEBUG_LOG(AMBASEBOARDDEBUG, "GC-AM: CMD 10, %02x (READ STATUS&SWITCHES)", ptr(1));
 							SPADStatus PadStatus;
 							memset(&PadStatus, 0 ,sizeof(PadStatus));
-							CPluginManager::GetInstance().GetPad(ISIDevice::m_iDeviceNumber)
+							CPluginManager::GetInstance().GetPad(0)
 								->PAD_GetStatus(ISIDevice::m_iDeviceNumber, &PadStatus);
 							res[resp++] = 0x10;
 							res[resp++] = 0x2;
@@ -312,7 +312,7 @@ int CSIDevice_AMBaseboard::RunBuffer(u8* _pBuffer, int _iLength)
 										for (i=0; i<nr_players; ++i)
 										{
 											SPADStatus PadStatus;
-											CPluginManager::GetInstance().GetPad(i)
+											CPluginManager::GetInstance().GetPad(0)
 												->PAD_GetStatus(i, &PadStatus);
 											unsigned char player_data[2] = {0,0};
 											if (PadStatus.button & PAD_BUTTON_START)
diff --git a/Source/Core/Core/Src/HW/SI_DeviceGCController.cpp b/Source/Core/Core/Src/HW/SI_DeviceGCController.cpp
index 50cde1edfe..457139b821 100644
--- a/Source/Core/Core/Src/HW/SI_DeviceGCController.cpp
+++ b/Source/Core/Core/Src/HW/SI_DeviceGCController.cpp
@@ -128,7 +128,7 @@ bool CSIDevice_GCController::GetData(u32& _Hi, u32& _Low)
 {
 	SPADStatus PadStatus;
 	memset(&PadStatus, 0, sizeof(PadStatus));
-	Common::PluginPAD* pad = CPluginManager::GetInstance().GetPad(ISIDevice::m_iDeviceNumber);
+	Common::PluginPAD* pad = CPluginManager::GetInstance().GetPad(0);
 	pad->PAD_GetStatus(ISIDevice::m_iDeviceNumber, &PadStatus);
 
 #if defined(HAVE_SFML) && HAVE_SFML
@@ -257,7 +257,7 @@ bool CSIDevice_GCController::GetData(u32& _Hi, u32& _Low)
 // SendCommand
 void CSIDevice_GCController::SendCommand(u32 _Cmd, u8 _Poll)
 {
-	Common::PluginPAD* pad = CPluginManager::GetInstance().GetPad(ISIDevice::m_iDeviceNumber);
+	Common::PluginPAD* pad = CPluginManager::GetInstance().GetPad(0);
 	UCommand command(_Cmd);
 
 	switch (command.Command)
diff --git a/Source/Core/Core/Src/PluginManager.cpp b/Source/Core/Core/Src/PluginManager.cpp
index 0c5ed2d6f7..8bbc72b226 100644
--- a/Source/Core/Core/Src/PluginManager.cpp
+++ b/Source/Core/Core/Src/PluginManager.cpp
@@ -76,17 +76,21 @@ CPluginManager::~CPluginManager()
 
 	for (int i = 0; i < MAXPADS; i++)
 	{
-		if (m_pad[i] && (OkayToInitPlugin(i) == -1))
+		if (m_pad[i])
 		{
-			INFO_LOG(CONSOLE, "Delete: %i\n", i);
 			delete m_pad[i];
+			m_pad[i] = NULL;
 		}
-		m_pad[i] = NULL;
 	}
 
 	for (int i = 0; i < MAXWIIMOTES; i++)
+	{
 		if (m_wiimote[i])
+		{
 			delete m_wiimote[i];
+			m_wiimote[i] = NULL;
+		}
+	}
 
 	delete m_video;
 }
@@ -139,15 +143,18 @@ bool CPluginManager::InitPlugins()
 	}
 
 	// Init wiimote
-	if (m_params->bWii) {
-		for (int i = 0; i < MAXWIIMOTES; i++) {
+	if (m_params->bWii)
+	{
+		for (int i = 0; i < MAXWIIMOTES; i++)
+		{
 			if (!m_params->m_strWiimotePlugin[i].empty())
 				GetWiimote(i);
 
 			if (m_wiimote[i] != NULL)
 				wiimote = true;
 		}
-		if (!wiimote) {
+		if (!wiimote)
+		{
 			PanicAlert("Can't init any Wiimote Plugins");
 			return false;
 		}
@@ -161,13 +168,13 @@ bool CPluginManager::InitPlugins()
 // for an explanation about the current LoadLibrary() and FreeLibrary() behavior.
 void CPluginManager::ShutdownPlugins()
 {
-	for (int i = 0; i < MAXPADS; i++) {
+	for (int i = 0; i < MAXPADS; i++)
+	{
 		if (m_pad[i])
 		{
 			m_pad[i]->Shutdown();
-			//delete m_pad[i];
+			FreePad(i);
 		}
-		//m_pad[i] = NULL;
 	}
 
 	for (int i = 0; i < MAXWIIMOTES; i++)
@@ -175,9 +182,8 @@ void CPluginManager::ShutdownPlugins()
 		if (m_wiimote[i])
 		{
 			m_wiimote[i]->Shutdown();
-			//delete m_wiimote[i];
+			FreeWiimote(i);
 		}
-		//m_wiimote[i] = NULL;
 	}
 
 	if (m_dsp)
@@ -224,7 +230,9 @@ CPluginInfo::CPluginInfo(const char *_rFilename)
 			PanicAlert("Could not get info about plugin %s", _rFilename);
 		// We are now done with this plugin and will call FreeLibrary()
 		delete plugin;
-	} else {
+	}
+	else
+	{
 		WARN_LOG(CONSOLE, "PluginInfo: %s is not a valid Dolphin plugin. Ignoring.", _rFilename);
 	}
 }
@@ -308,19 +316,6 @@ void *CPluginManager::LoadPlugin(const char *_rFilename, int Number)
 	return plugin;
 }
 
-/* Check if the plugin has already been initialized. If so, return the Id of
-   the duplicate pad so we can point the new m_pad[] to that */
-int CPluginManager::OkayToInitPlugin(int Plugin)
-{
-	// Compare it to the earlier plugins
-	for (int i = 0; i < Plugin; i++)
-		if (m_params->m_strPadPlugin[Plugin] == m_params->m_strPadPlugin[i])
-			return i;
-	
-	// No there is no duplicate plugin
-	return -1;	
-}
-
 PLUGIN_GLOBALS* CPluginManager::GetGlobals()
 {
 	return m_PluginGlobals;
@@ -386,15 +381,8 @@ Common::PluginPAD *CPluginManager::GetPad(int controller)
 		if (m_pad[controller]->GetFilename() == m_params->m_strPadPlugin[controller])
 			return m_pad[controller];
 	
-	// Else do this
-	if (OkayToInitPlugin(controller) == -1) {
-		m_pad[controller] = (Common::PluginPAD*)LoadPlugin(m_params->m_strPadPlugin[controller].c_str(), controller);
-		INFO_LOG(CONSOLE, "LoadPlugin: %i", controller);
-	}
-	else {
-		INFO_LOG(CONSOLE, "Pointed: %i to %i", controller, OkayToInitPlugin(controller));
-		m_pad[controller] = m_pad[OkayToInitPlugin(controller)];
-	}	
+	// Else load a new plugin
+	m_pad[controller] = (Common::PluginPAD*)LoadPlugin(m_params->m_strPadPlugin[controller].c_str());
 	return m_pad[controller];
 }
 
@@ -458,7 +446,8 @@ void CPluginManager::FreeDSP()
 
 void CPluginManager::FreePad(u32 Pad)
 {
-	if (Pad < MAXPADS) {
+	if (Pad < MAXPADS)
+	{
 		delete m_pad[Pad];
 		m_pad[Pad] = NULL;	
 	}
diff --git a/Source/Core/Core/Src/PluginManager.h b/Source/Core/Core/Src/PluginManager.h
index 134c389118..1d2fac10c2 100644
--- a/Source/Core/Core/Src/PluginManager.h
+++ b/Source/Core/Core/Src/PluginManager.h
@@ -60,7 +60,6 @@ public:
 	bool InitPlugins();
 	void ShutdownPlugins();
 	void ShutdownVideoPlugin();
-	int OkayToInitPlugin(int Plugin);
 	void ScanForPlugins();
 	void OpenConfig(void* _Parent, const char *_rFilename, PLUGIN_TYPE Type);
 	void OpenDebug(void* _Parent, const char *_rFilename, PLUGIN_TYPE Type, bool Show);
diff --git a/Source/Core/VideoCommon/Src/CommandProcessor.cpp b/Source/Core/VideoCommon/Src/CommandProcessor.cpp
index 7c0864d692..a9151af1b0 100644
--- a/Source/Core/VideoCommon/Src/CommandProcessor.cpp
+++ b/Source/Core/VideoCommon/Src/CommandProcessor.cpp
@@ -133,11 +133,6 @@ inline void WriteHigh(volatile u32& _reg, u16 highbits) {Common::AtomicStore(_re
 inline u16 ReadLow  (u32 _reg)  {return (u16)(_reg & 0xFFFF);}
 inline u16 ReadHigh (u32 _reg)  {return (u16)(_reg >> 16);}
 
-void UpdateInterrupts_Wrapper(u64 userdata, int cyclesLate)
-{
-	UpdateInterrupts();
-}
-
 void Init()
 {
 	m_CPStatusReg.Hex = 0;
@@ -161,7 +156,7 @@ void Init()
 
 	s_fifoIdleEvent.Init();
 
-    et_UpdateInterrupts = g_VideoInitialize.pRegisterEvent("UpdateInterrupts", UpdateInterrupts_Wrapper);
+//    et_UpdateInterrupts = g_VideoInitialize.pRegisterEvent("UpdateInterrupts", UpdateInterrupts_Wrapper);
 }
 
 void Shutdown()
@@ -187,7 +182,7 @@ void Read16(u16& _rReturnValue, const u32 _Address)
 		m_CPStatusReg.ReadIdle = fifo.CPReadIdle; // This seems not necessary though
 		m_CPStatusReg.Breakpoint = fifo.bFF_Breakpoint;
 		// Clear on Read
-		g_VideoInitialize.pSetInterrupt(INT_CAUSE_CP, false);
+		UpdateInterrupts(false);
 		
 		_rReturnValue = m_CPStatusReg.Hex;
 
@@ -358,14 +353,22 @@ void Write16(const u16 _Value, const u32 _Address)
 			{
 				// Instant Breakpoint and Interrupt, since we haven't implemented accurate BP on dual core
 				// Most likely the Read thread has already exceeded BP here, but it seems we are still cool
-				Common::AtomicStore(fifo.bFF_Breakpoint, tmpCtrl.BPEnable && tmpCtrl.CPIntEnable && tmpCtrl.GPReadEnable);
-				UpdateInterrupts();
+				if (tmpCtrl.BPEnable && tmpCtrl.CPIntEnable && tmpCtrl.GPReadEnable && tmpCtrl.GPLinkEnable)
+				{
+					Common::AtomicStore(fifo.bFF_Breakpoint, 1);
+					UpdateInterrupts(true);
+				}
+				else
+				{
+					Common::AtomicStore(fifo.bFF_Breakpoint, 0);
+				}
+				
 			}
 			else
 			{
 				// fifo.bFF_BPEnable is only used in single core
-				Common::AtomicStore(fifo.bFF_BPEnable, tmpCtrl.BPEnable && tmpCtrl.CPIntEnable && tmpCtrl.GPReadEnable);
-				if (!tmpCtrl.BPEnable || !tmpCtrl.CPIntEnable || !tmpCtrl.GPReadEnable)
+				Common::AtomicStore(fifo.bFF_BPEnable, tmpCtrl.BPEnable && tmpCtrl.CPIntEnable && tmpCtrl.GPReadEnable && tmpCtrl.GPLinkEnable);
+				if (!tmpCtrl.BPEnable || !tmpCtrl.CPIntEnable || !tmpCtrl.GPReadEnable || !tmpCtrl.GPLinkEnable)
 					Common::AtomicStore(fifo.bFF_Breakpoint, 0);
 			}
 
@@ -608,7 +611,7 @@ void CatchUpGPU()
 				{
 					//_assert_msg_(POWERPC,0,"BP: %08x",fifo.CPBreakpoint);
 					fifo.bFF_Breakpoint = 1;
-					UpdateInterrupts();
+					UpdateInterrupts(true);
 					break;
 				}
 			}
@@ -669,17 +672,24 @@ void UpdateFifoRegister()
 		CatchUpGPU();
 }
 
-void UpdateInterrupts()
+void UpdateInterrupts(bool active)
 {
-	DEBUG_LOG(COMMANDPROCESSOR, "Fifo Breakpoint Interrupt triggered");
-	g_VideoInitialize.pSetInterrupt(INT_CAUSE_CP, true);
+	DEBUG_LOG(COMMANDPROCESSOR, "Fifo Breakpoint Interrupt: %s", (active)? "Asserted" : "Deasserted");
+	g_VideoInitialize.pSetInterrupt(INT_CAUSE_CP, active);
 }
 
+/*
 void UpdateInterruptsFromVideoPlugin()
 {
 	g_VideoInitialize.pScheduleEvent_Threadsafe(0, et_UpdateInterrupts, 0);
 }
 
+void UpdateInterrupts_Wrapper(u64 userdata, int cyclesLate)
+{
+	UpdateInterrupts();
+}
+*/
+
 void SetFifoIdleFromVideoPlugin()
 {
 	s_fifoIdleEvent.Set();
diff --git a/Source/Core/VideoCommon/Src/CommandProcessor.h b/Source/Core/VideoCommon/Src/CommandProcessor.h
index 1a3a47ace8..668b2c2f34 100644
--- a/Source/Core/VideoCommon/Src/CommandProcessor.h
+++ b/Source/Core/VideoCommon/Src/CommandProcessor.h
@@ -148,8 +148,8 @@ void Write32(const u32 _Data, const u32 _Address);
 void CatchUpGPU();
 void GatherPipeBursted();
 void UpdateFifoRegister();
-void UpdateInterrupts();
-void UpdateInterruptsFromVideoPlugin();
+void UpdateInterrupts(bool active);
+//void UpdateInterruptsFromVideoPlugin();
 void SetFifoIdleFromVideoPlugin();
 
 bool AllowIdleSkipping();
diff --git a/Source/PluginSpecs/pluginspecs_pad.h b/Source/PluginSpecs/pluginspecs_pad.h
index 9373b7499d..fe8031f729 100644
--- a/Source/PluginSpecs/pluginspecs_pad.h
+++ b/Source/PluginSpecs/pluginspecs_pad.h
@@ -35,7 +35,6 @@ typedef struct
 {
 	HWND			hWnd;
 	TLog			pLog;
-    int				padNumber;
 } SPADInitialize;
 
 typedef struct
diff --git a/Source/Plugins/Plugin_PadSimple/Src/PadSimple.cpp b/Source/Plugins/Plugin_PadSimple/Src/PadSimple.cpp
index 71169a9500..c18e7da6d8 100644
--- a/Source/Plugins/Plugin_PadSimple/Src/PadSimple.cpp
+++ b/Source/Plugins/Plugin_PadSimple/Src/PadSimple.cpp
@@ -714,7 +714,6 @@ void Shutdown()
 	g_EmulatorRunning = false;
 
 #ifdef _WIN32
-	dinput.Free();
 	// Kill xpad rumble
 	XINPUT_VIBRATION vib;
 	vib.wLeftMotorSpeed  = 0;
@@ -722,6 +721,7 @@ void Shutdown()
 	for (int i = 0; i < 4; i++)
 		if (pad[i].bRumble)
 			XInputSetState(pad[i].XPadPlayer, &vib);
+	dinput.Free();
 #endif
 	SaveConfig();
 }