(This was reported for the Annex originally, where 3.9.1 is still latest, and looks like a bit that this person like to test everything with "Annex" in the name

.)
By the way (a bit related) for me on KDE (nvidia proprietary driver) even launching fullscreen MG with not the same screen resolution as general desktop's resolution might "screws up screen setup", not always but also it wasn't very rare, but since long time I am launching fullscreen MG with "resolution=resolution" then I don't know about does anything changed in this case.
I also remember some recommendation in some "debian's guide"(probably) that more preferred "default mode" is a "window mode" and there were some examples why, which were somehow related with this report.