When I run a wine app in fullscreen the top Unity panel is visible flickering through it on and off. The "Legacy fullscreen support" does not help, when running without Compiz (Unity 2d) everything is fine.
I found the solution - In CompizConfig Setting Manager go to "Composite" and check "Unredirect fullscreen windows". Hope this helps others having the same problem.
Yeah... That's an old problem with compositing, there isn't much you can do about it. Other than opening up 'winecfg' and tabbing over to Graphics. Check "Emulate a Virtual Desktop" and run it in a 800x600 (or resolution of your choice) window.