Comment 4 for bug 1414988

Okay, one more observation:
The whole thing can be rectified, post-login, by turning that external secondary monitor (the 'star'ed one with the menu on it) off. then all windows automatically pop back to the build-in monitor, then turning that external monitor off in the 'Display and Monitor' in 'System Settings' by removing the tick on that monitor, 'apply', adding back that tick, 'star'ing it again (to indicate that it should carry the menu), 'apply'.
Then the geometry is as expected.
From all this, I dare to suspect that the trouble comes in through the timing(s) at logon. It looks like everything is okay, when the external display comes up after the build-in one, gets activated, and then receives the menu.