http://bugs.winehq.org/show_bug.cgi?id=12353
--- Comment #1 from Giuseppe Bilotta giuseppe.bilotta@gmail.com 2008-04-04 19:01:45 --- Created an attachment (id=11856) --> (http://bugs.winehq.org/attachment.cgi?id=11856) Possible patch to fix the problem
The problem seems to be that the Bat's main window is not marked as WS_EX_APPWINDOW, and it has an owner (I think it's the tray icon but I'm not sure). The Bat! itself has an option to skip the taskbar when the tray icon is always on.
The proposed patch doesn't skip the taskbar unless the owned window is explicitly set as CHILD or POPUP window.