I used the guide to auto start the MM on boot. The pi3 boots up fully and the MM turns the entire screen black, however when the MM loads it only uses the top portion of the screen and overlaps all of the modules. When starting the mirror from the terminal it works exactly as it should. Only when Auto start is configured it gives me the half overlapped screen.
It seems to me that a small white window pops up, then is replaced by the full screen mode. And the MM is only being loaded on the small window.