https://bugs.winehq.org/show_bug.cgi?id=37765
--- Comment #5 from Stefan Dösinger stefan@codeweavers.com --- Metacity and the window managers forked from it break when XIconifyWindow is called on a window that does not set MWM_FUNC_MINIMIZE. I have reported the issue to Marco (https://github.com/mate-desktop/marco/issues/166). Mutter in Gnome Shell seems to have so many issues with fullscreen handling (the window doesn't even show up for me) that I don't know where to start reporting bugs :-\ .
Since 45d530461bf29c953f5f4532cc0e917b4c4fc296 wined3d minimizes the game window on focus loss like windows does. This probably caused your problems.