diff --git a/pcsx2/gui/AppConfig.cpp b/pcsx2/gui/AppConfig.cpp
index ddf65394c0..a374bc50fa 100644
--- a/pcsx2/gui/AppConfig.cpp
+++ b/pcsx2/gui/AppConfig.cpp
@@ -869,8 +869,9 @@ bool AppConfig::IsOkApplyPreset(int n)
 	//Console.WriteLn("Applying Preset %d ...", n);
 
 	//Have some original and default values at hand to be used later.
-	Pcsx2Config::GSOptions  original_GS = EmuOptions.GS;
-	AppConfig::FramerateOptions	original_Framerate = Framerate;
+	Pcsx2Config::GSOptions        original_GS = EmuOptions.GS;
+	AppConfig::FramerateOptions	  original_Framerate = Framerate;
+	Pcsx2Config::SpeedhackOptions original_SpeedHacks = EmuOptions.Speedhacks;
 	AppConfig				default_AppConfig;
 	Pcsx2Config				default_Pcsx2Config;
 
@@ -880,7 +881,7 @@ bool AppConfig::IsOkApplyPreset(int n)
 	//			2. The panels should not apply values which the presets don't control if the value is initiated by a preset.
 	//			Currently controlled by the presets:
 	//			- AppConfig:	Framerate (except turbo/slowmo factors), EnableSpeedHacks, EnableGameFixes.
-	//			- EmuOptions:	Cpu, Gamefixes, SpeedHacks, EnablePatches, GS (except for FrameLimitEnable, VsyncEnable and ManagedVsync).
+	//			- EmuOptions:	Cpu, Gamefixes, SpeedHacks (except mtvu), EnablePatches, GS (except for FrameLimitEnable, VsyncEnable and ManagedVsync).
 	//
 	//			This essentially currently covers all the options on all the panels except for framelimiter which isn't
 	//			controlled by the presets, and the entire GSWindow panel which also isn't controlled by presets
@@ -908,7 +909,7 @@ bool AppConfig::IsOkApplyPreset(int n)
 	EmuOptions.Gamefixes			= default_Pcsx2Config.Gamefixes;
 	EmuOptions.Speedhacks			= default_Pcsx2Config.Speedhacks;
 	EmuOptions.Speedhacks.bitset	= 0; //Turn off individual hacks to make it visually clear they're not used.
-
+	EmuOptions.Speedhacks.vuThread	= original_SpeedHacks.vuThread; // MTVU is not modified by presets
 
 	//Actual application of current preset over the base settings which all presets use (mostly pcsx2's default values).
 	//The presets themselves might need some voodoo tuning to be even more useful. Currently they mostly modify Speedhacks.
diff --git a/pcsx2/gui/Panels/SpeedhacksPanel.cpp b/pcsx2/gui/Panels/SpeedhacksPanel.cpp
index 0052b1a0de..6a4e1ccd5c 100644
--- a/pcsx2/gui/Panels/SpeedhacksPanel.cpp
+++ b/pcsx2/gui/Panels/SpeedhacksPanel.cpp
@@ -269,9 +269,7 @@ Panels::SpeedHacksPanel::SpeedHacksPanel( wxWindow* parent )
 
 void Panels::SpeedHacksPanel::EnableStuff( AppConfig* configToUse )
 {
-	//Console.WriteLn("SpeedHacksPanel::EnableStuff: Using %s", configToUse?"Object":"NULL");
 	if( !configToUse ) configToUse = g_Conf;
-	//Console.WriteLn("SpeedHacksPanel::EnableStuff: EnabledPresets: %s", configToUse->EnablePresets?"true":"false");
 	wxSizerItemList& items( s_table->GetChildren() );
 
 	wxSizerItemList::iterator it	= items.begin();
@@ -279,7 +277,7 @@ void Panels::SpeedHacksPanel::EnableStuff( AppConfig* configToUse )
 
 	while( it != end )
 	{
-		(*it)->GetWindow()->Enable( m_check_Enable->GetValue() && !configToUse->EnablePresets);
+		(*it)->GetWindow()->Enable( m_check_Enable->GetValue());
 		++it;
 	}
 }
@@ -295,19 +293,22 @@ void Panels::SpeedHacksPanel::ApplyConfigToGui( AppConfig& configToApply, int fl
 	const bool enabled = configToApply.EnableSpeedHacks;
 	Pcsx2Config::SpeedhackOptions& opts=configToApply.EmuOptions.Speedhacks;
 
-	m_check_Enable		->SetValue( !!enabled );
+	m_check_Enable		->SetValue( !!enabled ).Enable(!configToApply.EnablePresets);
 
 	m_slider_eecycle	->SetValue( opts.EECycleRate + 1 );
 	m_slider_vustealer	->SetValue( opts.VUCycleSteal );
+	m_slider_eecycle->Enable(!configToApply.EnablePresets);
+	m_slider_vustealer->Enable(!configToApply.EnablePresets);
 
 	SetEEcycleSliderMsg();
 	SetVUcycleSliderMsg();
 
-	m_check_vuFlagHack	->SetValue(opts.vuFlagHack);
-	m_check_vuThread	->SetValue(opts.vuThread);
-	m_check_intc		->SetValue(opts.IntcStat);
-	m_check_waitloop	->SetValue(opts.WaitLoop);
-	m_check_fastCDVD	->SetValue(opts.fastCDVD);
+	m_check_vuFlagHack	->SetValue(opts.vuFlagHack).Enable(!configToApply.EnablePresets);
+	if( !(flags & AppConfig::APPLY_FLAG_FROM_PRESET) )
+		m_check_vuThread	->SetValue(opts.vuThread);
+	m_check_intc		->SetValue(opts.IntcStat).Enable(!configToApply.EnablePresets);
+	m_check_waitloop	->SetValue(opts.WaitLoop).Enable(!configToApply.EnablePresets);
+	m_check_fastCDVD	->SetValue(opts.fastCDVD).Enable(!configToApply.EnablePresets);
 
 	EnableStuff( &configToApply );
 
@@ -315,8 +316,6 @@ void Panels::SpeedHacksPanel::ApplyConfigToGui( AppConfig& configToApply, int fl
 	Layout();
 
 	//Console.WriteLn("SpeedHacksPanel::ApplyConfigToGui: EnabledPresets: %s", configToApply.EnablePresets?"true":"false");
-
-	this->Enable(!configToApply.EnablePresets);
 }