http://bugs.winehq.org/show_bug.cgi?id=24222
--- Comment #1 from Dmitry Timoshkov dmitry@codeweavers.com 2010-08-31 10:16:06 CDT --- Does support Mutter the dialog type windows?
Try to disable _NET_WM_WINDOW_TYPE_DIALOG in dlls/winex11.drv/window.c and see if that helps.
In any case this sounds like a Mutter bug, since this works just fine under other WMs.