http://bugs.winehq.org/show_bug.cgi?id=27779
--- Comment #32 from Kaj F. linuxgeek1994@gmail.com 2011-07-25 13:33:44 CDT --- (In reply to comment #31)
yes when running the game in windowed mode the cursor is not present, atleast in counter-strike source.
That would explain why I have not seen this issue in Team Fortress 2 or my other Source games, as I have been running them in windowed mode as well, so I don't have to disable my second monitor all the time.
When running these games in fullscreen mode, however, I do see this issue in all of my Steam games.