diff --git a/pcsx2/gui/AppInit.cpp b/pcsx2/gui/AppInit.cpp
index 2149352eb7..d5eccf4e21 100644
--- a/pcsx2/gui/AppInit.cpp
+++ b/pcsx2/gui/AppInit.cpp
@@ -236,7 +236,7 @@ void Pcsx2App::OpenProgramLog()
 
 void Pcsx2App::AllocateCoreStuffs()
 {
-	if( AppRpc_TryInvokeAsync( &Pcsx2App::OpenMainFrame ) ) return;
+	if( AppRpc_TryInvokeAsync( &Pcsx2App::AllocateCoreStuffs ) ) return;
 
 	CpuCheckSSE2();
 	SysLogMachineCaps();
@@ -523,10 +523,19 @@ bool Pcsx2App::OnInit()
 		// -------------------------------------
 		if( Startup.ForceConsole ) g_Conf->ProgLogBox.Visible = true;
 		OpenProgramLog();
-
 		if( m_UseGUI ) OpenMainFrame();
-
 		AllocateCoreStuffs();
+		
+		if( Startup.SysAutoRun )
+		{
+			// Notes: Saving/remembering the Iso file is probably fine and desired, so using
+			// SysUpdateIsoSrcFile is good(ish).
+			// Saving the cdvd plugin override isn't desirable, so we don't assign it into g_Conf.
+
+			g_Conf->EmuOptions.UseBOOT2Injection = !Startup.NoFastBoot;
+			SysUpdateIsoSrcFile( Startup.IsoFile );
+			sApp.SysExecute( Startup.CdvdSource );
+		}
 	}
 	// ----------------------------------------------------------------------------
 	catch( Exception::StartupAborted& ex )		// user-aborted, no popups needed.
diff --git a/pcsx2/gui/AppMain.cpp b/pcsx2/gui/AppMain.cpp
index 8695b14236..57ed672dad 100644
--- a/pcsx2/gui/AppMain.cpp
+++ b/pcsx2/gui/AppMain.cpp
@@ -799,6 +799,12 @@ void Pcsx2App::OnGsFrameClosed( wxWindowID id )
 
 	CoreThread.Suspend();
 	m_id_GsFrame = wxID_ANY;
+
+	if( !m_UseGUI )
+	{
+		// [TODO] : Prompt user before exiting, k thx. :)
+		PrepForExit();
+	}
 }
 
 void Pcsx2App::OnProgramLogClosed( wxWindowID id )
diff --git a/pcsx2/gui/MainMenuClicks.cpp b/pcsx2/gui/MainMenuClicks.cpp
index bffb47baff..a2882d94f6 100644
--- a/pcsx2/gui/MainMenuClicks.cpp
+++ b/pcsx2/gui/MainMenuClicks.cpp
@@ -125,7 +125,7 @@ wxWindowID SwapOrReset_Iso( wxWindow* owner, IScopedCoreThread& core_control, co
 {
 	wxWindowID result = wxID_CANCEL;
 
-	if( g_Conf->CdvdSource == CDVDsrc_Iso && isoFilename == g_Conf->CurrentIso )
+	if( (g_Conf->CdvdSource == CDVDsrc_Iso) && (isoFilename == g_Conf->CurrentIso) )
 	{
 		core_control.AllowResume();
 		return result;