What does gpu-manager do?

gpu-manager is software that creates a xorg.conf for you.

It is a bug in gpu-manager: it recreates xorg.org on each boot. Let Ubuntu do its thing and disable gpu-manager as you already mentioned.

Have a look at /var/log/gpu-manager.log for any messages. If you add yourself to the bug below (that claims to be fixed but comments at the bottom disagree...) you need that log.

And this bug report has the work-around you describe (by Nash Kaminski on 2014-04-22):

gpu-manager is responsible for overwriting your X config file. Commenting out the "start on" lines at the top of gpu-manager's upstart script located at /etc/init/gpu-manager.conf will temporarily disable gpu-manager and prevent xorg.conf from being changed.