Cause confirmed: Contrary to what I said before, it is the file manager handling the desktop which somehow glitches gnome-shell. Switching that off and logging back again solves the issue; switching that on and logging back again triggers the bug.
Another side-effect of this bug is that the lockdown screen doesn't fade into the screensaver after timing out or pressing the Esc key, but it just shows the (GDM, I presume) background hiding the password dialog. On the other hand, Ubuntu users have been experiencing some similar: http://ubuntuforums.org/showthread.php?t=2088736 Sorry for all the "spam"; I've been looking at this by chunks, but now I think the description and cause of the bug are pretty clear.
