I get the windows and hotbars dissappears in windowed mode from time to time too. It happens when I lower the quality settings. What I have found works to fix it, for me at least, without going to back to high quality is making sure that Enable Bloom Effect and Heat Shimmer are both CHECKED under atomospheric effects. I am using Windows 7, but I don't usually lower my graphics settings so I don't know if its specific to the OS or just something I've never noticed before. It may not do anything to help your case but it certainly can't hurt. Good luck getting it resolved.
