When running a program in wine, and I use a hotkey combo to either switch desktops or open another program (example: to bring forward my fullscreen terminal), the modifier keys are still depressed, according to wine, when I switch back to the wine window. I did some tests, and found that when switching desktops away from wine with a hotkey with modifiers, and then switching back with a method that doesn't require modifiers, the problem shows up. When I do the reverse, switching away without modifier keys, then switching back with them, the problem is gone. This leads me to think it's an issue with wine not receiving the correct events from X, but I'm not sure how to debug this. It sounds an awful lot like this bug that was fixed in wine several years ago: http://bugs.winehq.org/show_bug.cgi?id=1990 I'm running Archlinux, 64 bit, and everything is up-to-date.
