http://bugs.winehq.org/show_bug.cgi?id=1990
------- Additional Comments From Speeddymon@gmail.com 2006-30-03 12:09 ------- This appears to be due to the fact that both wine and the x server are catching the combo. wine thinks that you are trying to send a ctrl+ whatever command to the windows app, and so catches the ctrl pressed event, but then when you press the Fx the x server steps in and switches the desktop for you. A good comparison is if you are pressing the ctrl button in wine, and then somehow you suspend the wine process. You can let go of ctrl, but because it was pressed when you suspended it, wine will still think it is pressed when you unsuspend it.. The only way I can think to stop this is to press control again after you switch back to wine, and it might catch the ctrl released. That or make sure you aren't sending commands to wine, by clicking on a blank area od the desktop, before you do the desktop switch.
For right now, I don't think this is possible to fix... Your best workaround is to maybe change the hotkeys used to switch desktops, or just not use hotkeys to switch desktops, since windows doesn't really support virtual desktops anyways..