http://bugs.winehq.org/show_bug.cgi?id=23543
--- Comment #14 from Jonathan Strander mblackwell1024@gmail.com 2012-06-21 23:23:53 CDT --- This seems to have reared its ugly head when playing Batman Arkham City in Gnome Shell (using 1.5.6 on Gnome Shell 3.4) fullscreen. Starting the game seems fine but after the loading screen there's only sound and no window listed. Switching to Metacity allows the game to overlap all other contents. I noted that telling the game to run Windowed also placed the window behind everything but it did show up in the Window List (however it would only run at 800x600, which is a separate bug and not necessarily one from Wine).
http://store.steampowered.com/app/57400/?snr=1_7_suggest__13
There's a link to a demo on Steam. Hopefully it should exhibit the same behavior.