Testing here, Fluxbox, amd64. When running a program in wine, after switching to another desktop and switching back to the wine program, the program window has disappeared somewhere in the background. The shortcut for cycling through programs in the same desktop brings it back.
As far as I can find, it seems to be caused by a certain interaction between wine and certain window managers, Fluxbox among them, and not with all programs installed with wine. It appears to be an old bug, which should have been fixed in wine 1.2. But this is wine 1.8! It is also mentioned here: http://marc.info/?l=wine-devel&m=108758530429491&w=2 "Wine window disappears from virtual desktop!" Not being an expert, I'm not sure how to apply this patch, and moreover, this message, too, is very old (2004). Anyone else having this, and is there a fix?