https://bugs.winehq.org/show_bug.cgi?id=38786
--- Comment #1 from Jason jasonwinter@hotmail.com --- I can see there was a workaround written in 2008 to fix other software that experienced an issue like this:
https://www.winehq.org/pipermail/wine-patches/2008-April/052861.html
I think it changed the tool-window priority so WS_DLGFRAME & WS_EX_DLGMODALFRAME windows used x11drv_atom(_NET_WM_WINDOW_TYPE_DIALOG) before reverting to the existing mode that has problems.
In my case, this won't work - the window I am using has no frame, it's just the clipping window [undetailed window] of a Direct-X VMR9 video renderer, so it looks "clean" while watching videos.