Could it be video card getting stuck between switching states from 3D to 2D (or, like ATi's drivers that like to flicker the screen a few times on startup with some cards and systems)?
What GPU do you have? And does it have the recentest drivers?
The only thing I've ever noticed with FS2_Open having residing side effects on display was if it was using it's own gamma calibration and quit inappropriately, the FS2_Open-affected gamma setting could stay behind... which is why I play with the
-no_set_gamma option enabled. Probably unrelated, but then again, I've seen stranger things with computers.
Also. Does this happen every time you quit FS2_Open, or only with certain conditions? Or seemingly randomly? What build(s) are giving the problem? Try to reproduce the problem. Run a debug build. Try windowed mode (crapsucks not being able to play in full screen, but if that's the only way you could use it, it's always an option... playing on 1280x720 resolution isn't too bad after all (at least if you ask UbiSoft, regarding Assassin's Creed on PC...
).