http://bugs.winehq.org/show_bug.cgi?id=27232
--- Comment #9 from sep16@psu.edu 2012-03-14 09:54:16 CDT --- When I had experienced this problem last year (comment #1 above), I walked back through the minor revisions until I was able to Alt-Tab switch without Alt sticking. The version I landed on was 1.3.14, so I left it at that.
I've recently switched to vim for my primary editor, so I don't use Wine as much. However, I just fired up wine-1.4 under Gnome 3, and I was unable to get the Alt key to stick while switching windows, with or without focus-follows-mouse.
(I also had the "click to refocus" problem Michal just mentioned, but I blamed it on switching to XMonad.)