Comment 101 for bug 1292398

Same problem here after upgrading three days ago from Ubuntu 14.04.4 (that worked) to 16.04.1 (that's broken as explained below).

Desktop Environment: GNOME-Flashback:Unity (gnome-flashback-metacity)
Dual screen, notebook + external VGA monitor.
NVidia Quadro FX 770M, 3.3.0 NVIDIA 340.96

I set the primary monitor to the notebook screen using nvidia-settings, and the setting stuck across logout: I see the gnome panel properly moving to the notebook screen when the Gnome GUI comes up after logout and reboot.

OTOH, my notebook is positioned to the right of my VGA monitor, and that's where the problem starts. The system insists on placing the notebook built-in screen to the left of the monitor.

If I set the primary monitor (notebook built-in screen) to the right of the VGA screen using nvidia-settings, I get what I want for the current session. But this setting is lost after the next session logout (or reboot for that matter).

If alternately, I set the primary monitor (notebook built-in screen) to the right of the VGA screen using "System Settings / Displays", I get what I want for the session, but this setting is also lost after the next logout (reboot).

The trick suggesting at #39 doesn't work for me (to start with, I have no etc/gnome-setting-daemon/xrandr on my system)

To add insult to injury, the upgrade also brought me a similar problem with the alsamixer settings: They are set to some default muted values that makes the machine totally silent at each session start, and whatever way I set them, they are reset to the same muted default values upon the next logout / login.
Not sure whether I also owe this to gnome-shell, but that's what I suspect.
I use "sudo alsactl" to manually handle the problem and reload the proper alsamixer value, but I hate it.

I have so far not found any simple, reliable fix or workaround for either problem. <sigh>