perhaps this is useful for somebody:
I've found that Aerofly FS2 runs very well in windowed mode. You can even fold it down, let it fly and surf in the net.
And there are no issues with the graphics when I unfold it on my machine. It just pops up.
To stop the full screen mode simply change the entry at the top of the main.mcf in c:\users\documents\aerofly fs2
from "true" to "false".