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 9fc7208ddb..fd25108a5e 100644
--- a/Source/Core/Core/HotkeyManager.cpp
+++ b/Source/Core/Core/HotkeyManager.cpp
@@ -157,6 +157,7 @@ static u32 hotkeyDown[3];
 static HotkeyStatus hotkey;
 
 static InputConfig s_config("Hotkeys", _trans("Hotkeys"), "Hotkeys");
+
 InputConfig* GetConfig()
 {
 	return &s_config;
@@ -170,10 +171,14 @@ void GetStatus()
 	((HotkeyManager*)s_config.controllers[0])->GetInput(&hotkey);
 }
 
-bool IsReady()
+bool IsEnabled()
 {
-	std::unique_lock<std::recursive_mutex> lk(s_config.controls_lock, std::try_to_lock);
-	return lk.owns_lock();
+	return enabled;
+}
+
+void Enable(bool enable_toggle)
+{
+	enabled = enable_toggle;
 }
 
 bool IsPressed(int Id, bool held)
@@ -209,6 +214,13 @@ void Initialize(void* const hwnd)
 
 	for (unsigned int i = 0; i < 3; ++i)
 		hotkeyDown[i] = 0;
+
+	enabled = true;
+}
+
+void LoadConfig()
+{
+	s_config.LoadConfig(true);
 }
 
 void Shutdown()
diff --git a/Source/Core/Core/HotkeyManager.h b/Source/Core/Core/HotkeyManager.h
index 6095db4906..bd76395046 100644
--- a/Source/Core/Core/HotkeyManager.h
+++ b/Source/Core/Core/HotkeyManager.h
@@ -32,9 +32,13 @@ namespace HotkeyManagerEmu
 {
 	void Initialize(void* const hwnd);
 	void Shutdown();
+	void LoadConfig();
 
 	InputConfig* GetConfig();
 	void GetStatus();
-	bool IsReady();
+	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 9352dcb367..b6b28a57f2 100644
--- a/Source/Core/DolphinWX/Frame.cpp
+++ b/Source/Core/DolphinWX/Frame.cpp
@@ -1263,7 +1263,7 @@ const CGameListCtrl *CFrame::GetGameListCtrl() const
 
 void CFrame::PollHotkeys(wxTimerEvent& event)
 {
-	if (!HotkeyManagerEmu::IsReady())
+	if (!HotkeyManagerEmu::IsEnabled())
 		return;
 
 	if (Core::GetState() == Core::CORE_UNINITIALIZED || Core::GetState() == Core::CORE_PAUSE)
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index 7ab7e9523c..04534a48fb 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"
@@ -1366,27 +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
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();