https://bugs.winehq.org/show_bug.cgi?id=50064
--- Comment #2 from Alexandr Oleynikov sashok.olen@gmail.com --- The patchset that is causing the issue is winex11-_NET_ACTIVE_WINDOW. If I disable it (along with winex11-WM_WINDOWPOSCHANGING since it depends on the former) the transparent window isn't present.