I am trying to understand what gpu-manager actually does. My searching has only found to disable it in grub and comment out gpu-manager.conf due to it overwriting xorg.conf. I am running 14.04 Xubuntu, 3 Nvidia 970's and their binary driver. Thanks!
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.
gpu-manageris 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.confwill temporarily disable
xorg.conffrom being changed.