[Wine] Inconsistent virtual desktop behavior (Ubuntu)

[Tpolich]

While running wine in a virtual desktop set to the same resolution of my screen it alway used to cover the top and bottom bars used by Ubuntu but presently for some reason the top and bottom bars are now coming out on top. 

Bars on top (normally happens now)
http://i346.photobucket.com/albums/p419/tpolich/whatnormalyhappens.png

Virtual desktop on top (always used to happen but now only does after a few wine restarts)
http://i346.photobucket.com/albums/p419/tpolich/whatiwantittobelike.png

I was wondering if anyone knows how to change something in any way that would make the virtual desktop on top. I have already tried the really simple things like right click on setting "Always on top" it didn't do anything.

Thank you for any help in advance.