http://bugs.winehq.org/show_bug.cgi?id=12441
--- Comment #2 from Dan Kegel dank@kegel.com 2008-04-09 01:59:31 --- Thanks, Dmitry :-)
Yes. The main problem is that the "Libraries" tab is overloaded. By default it controls the systemwide default library overrides, but if you go over to the Applications tab and add an application, the Libraries tab magically and silently changes meaning to cover just overrides of that application.
The quickest fix would be to show the currently selected application in the Libraries tab as well, I think.