http://bugs.winehq.org/show_bug.cgi?id=58443
--- Comment #17 from zlice zlice@crtdrift.us --- i know Withdrawn stuff was changed by a hack for cinnamon a while back, and it doesn't check if the window manager is cinnamon through xdg env vars or anything like firefox does for example, it just does it (withdraws windows).
from what i remember, the person who investigate the withdraw hack breaking fluxbox submitted a patch to fluxbox and said it wasn't "exactly a X spec but many WMs withdraw when iconified". although i'm not sure what common practice was for old style iconify being "add icon on the desktop".
the fluxbox bit you mentioned with active window _NET_ACTIVE_WINDOW being changed:
other bugs ive witnessed what seems like thread races for conditions like this. wine says "focus me" or whatever state change - then if you add prints or turn on debug which slows things down - whatever issue with focus/active window/state change goes away.
other changes like the watch_dogs QS_POSTMESSAGE adding(or-ing) QS_SENDMESSAGE seem to mess with focus too but i really dont understand what that is in windows world, but it seems like that is a wait for focus. im sure that plays in somehow.
have never really tested "Allow the window manager to control the windows" - but i assume it will completely change how things behave. may check it out just for curiosity, but i can see it introducing more weirdness.