Sorry if this is stating the obvious, but I've switched back from gnome
to unity and that is definitely not affected in the same manner; so it's
definitely gnome-shell specific.
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Public bug reported:
When playing a steam game in "fullscreen" (in this case stellaris) if I
alt-tab out and then back the game is no longer full screen and a
portion the size of the menu bar at the top is reserved, not showing the
menu just a portion of the background colour. Also after this
