http://bugs.winehq.org/show_bug.cgi?id=14029
--- Comment #1 from Vitaliy Margolen vitaliy@kievinfo.com 2008-06-20 22:35:43 --- Are you using "focus follows mouse" focus rule? It's not compatible with Wine.
Windows does not offer anything like that. And by default pop-up windows appear to the right and bottom of the pointer.