Some patches were committed to wine recently to make it use _NET_WM_STATE_FULLSCREEN for fullscreen apps. These patches appear to work in kwin but not metacity (I was using firefox as a test). In metacity, it appears wine recognizes that it needs to make a window fullscreen and send the appropriate message, but nothing happens (panels are still on top of firefox in fullscreen mode).
I've mentioned this on wine's bug (http://bugs.winehq.org/show_bug.cgi?id=3312), but I suspect it's probably caused by some quirk in metacity that wine triggers by doing some rather odd things itself. That's why I've CC'd the metacity-devel list (to which I and probably anyone on any wine mailing lists are not subscribed).
So, uh, metacity people, under what circumstances would metacity be likely to put a window that had sent the proper _NET_WM_STATE_ADD message for _NET_WM_STATE_FULLSCREEN behind panels?