Comment 4 for bug 876999

More info (I typed too soon before)

I can now confirm that typing "killall nautilus" will fix all application windows until a nautilus instance is loaded (eg opening the home folder). This will cause all other windows to become invisible again. However, retyping killall nautilus will fix again.

Obviously this is only a debugging workaround as the user cannot still use nautilus. It seems, therefore, that this is related to Compiz's interactions with Nautilus under Unity (3D).