https://bugs.winehq.org/show_bug.cgi?id=51526
--- Comment #9 from Rafał Mużyło galtgendo@o2.pl --- I believe I've stumbled upon something similar.
An app work fine if fullscreen, but if you switch it to windowed, its window 'disappears'. By that I mean it seems to be moved partially off screen and unmapped - this is learned via xwininfo. If wmctrl is used to activate it, it shows up, but refuses to accept mouse input (not sure about the keyboard).
Problem also happens if you get it to start windowed.