Apple has posted a support article confirming that if you use .Mac Sync and Spaces, you might lose windows.

Basically, the bug occurs if two computers have Spaces, but different Spaces settings. Say, one computer has two spaces, and the other has four. If one computer has a window in fourth space, it won’t show up on the other computer, since the other computer only has the first and second space.

This is because .Mac Sync sends window location preferences between computers. Now, Spaces is supposed to kick windows off of a space if you remove it, but that self-regulation doesn’t exist if Spaces doesn’t know that a space was removed.

It’s a bug, and Apple’s working on it. The best fix right now is that if you use Spaces, make sure all your systems that sync via .Mac share the same settings.