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I think what's happening here might be caused by a bit of insanity which Microsoft put into Win2000/XP. Previously, the OS kept track of which buffer was being displayed, the front or back buffer. For no good reason at all, this was removed, destroying my ability to bring up requesters on top of the main screen (half the time they would appear on the wrong buffer underneath the main screen, making them invisible).
3D glasses rely on the ability to know which buffer was which for left-eye/right-eye display. All you can do now is guess which buffer you are writing to, paint a frame, and tell the OS to switch buffers. Then you assume that it actually did switch buffers and start painting to the other one, but this is not a fool-proof assumption. If they didn't get switched, then the left and right eyes would get reversed, maybe for a frame or two, maybe for a long period.
I haven't had a chance to play with DX9 yet, but I'm hoping that it fixed this problem.
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