At first I thought this was a problem with my app, but it seems to be happening in any app (though interestingly, not the home screen) in the gingerbread emulator.
T
Actually, I have run into that problem occasionally before, though it does seem to get progressively worse with each passing tools release. There is nothing wrong with your installation or how you are using the program, AFAIK. You might try using Ctrl-F12 to switch back rather than Ctrl-F11 and see if that improves matters. I think the problem may stem from the emulator trying to emulate four-way orientation, but that is just a guess.