When I run the WINE App "StarCraft: Brood War," with the Winecfg > Graphics > Window Settings as "Allow the window manager to control the windows" in Compiz 0.5.5, the panels appear on top of the fullscreen application.
This does not happen when I use the Metacity.
When I run Metacity, the following message appears when I attempt to run the game StarCraft: Brood War with WINE.
Window manager warning: Treating resize request of legacy application 0x3800001 (Brood War) as a fullscreen request
Created attachment 11263 [details]
Screenshot of bug
The Compiz Fusion plugin "Workarounds" does exactly that.