Can you post a screenshot?
Normally when running a windowed program at your monitor's native resolution, the only problem would be the window borders, but it sounds like you're having another issue besides that.
By the way, it's not perfect, but the game still plays quite well at 1280x768 windowed on my 1680x1050 monitor. (I don't have any crashes. The Windows 7 beta just doesn't support fullscreen OpenGL properly).
Sidebar: After checking what resolution I run the game in, I clicked Exit, then alt-tabbed into Firefox. Upon doing so, the game paused itself and would not finish exiting until I alt-tabbed back. I understand the logic of pausing the game when the window doesn't have focus, but doing so while it's in the process of shutting down seems a tad on the silly side.