Comment 67 for bug 1288572

sgon00, the layout issues with gnome-shell is not a bug really, gnome-shell will put the panel on the primary display which according to the xrandr output above is the non-existant VGA-0 display.

The xrandr output in #22 was correct, so something must have changed since then. This will be unrelated to GNOME, so you should file a new bug for this issue (against nvidia-prime I guess) with xrand -q and xrandr --listoutputproviders output and Xorg logs

Not sure about #66, are you saying this only happens if you reload gnome-shell and then reboot? or does it always happen on every reboot?