If you get a flickering black screen with "Mission file can't load" or some such when you load the sim, then one of two things has happened:
1. You deleted or invalidated the aircraft you were flying last in QC, and as it reloads you last QC aircraft on launch, it gets stuck.
2. Your "frontend.xml" file is invalid. This can be remade easily in Mission Builder and then hand-edited to fit; besically, as you can see from my last post, it's nothing more than a mini-mission file. You can change the aircraft, airfield, weather and time to suit your own taste.
As far as I know, these are the only two circumstances where you get the "Mission file failed..." screen.