Comment 70 for bug 1288572

I think the non-existent primary display (VGA-0) is still causing troubles. I suspect once that is fixed things will work properly, so you should file a bug for that one.

Also the settings you applied when in a gnome-shell user session, won't apply for gdm.

I occasionally see that flickering on my second monitor, this is also possibly a bug in the Nvidia driver.