pcsx2: Fix autorun when commandline and current CDVD options differ

Fixes an issue where the game will either boot the wrong CDVD source or
fail to boot if the current CDVD option doesn't match the option
specified in the command line.

pcsx2/gui/AppInit.cpp

@@ -495,11 +495,8 @@ bool Pcsx2App::OnInit()
 
 		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;
+			g_Conf->CdvdSource = Startup.CdvdSource;
 			SysUpdateIsoSrcFile( Startup.IsoFile );
 			sApp.SysExecute( Startup.CdvdSource );
 		}