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>

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https://bugs.launchpad.net/bugs/1292398

Title:
  Second screen position isn't saved from one session to another

Status in elementary OS:
  Fix Released
Status in gnome-settings-daemon:
  Unknown
Status in gnome-shell:
  Confirmed
Status in Ubuntu GNOME:
  Confirmed
Status in Ubuntu GNOME trusty series:
  Confirmed
Status in Ubuntu GNOME xenial series:
  Confirmed
Status in Ubuntu GNOME Flashback:
  Confirmed
Status in Unity:
  New
Status in gnome-settings-daemon package in Ubuntu:
  Triaged
Status in gnome-shell package in Ubuntu:
  Triaged

Bug description:
  (Noticed on Ubuntu 14.04 beta 1 GNOME)
  At work I have a second screen, which I prefer to virtually put on the left 
side of my laptop screen.
  Using gnome-control-center I can change the position of the second without 
problem.
  But when I disconnect the second screen (to work on another place) and then 
connect it again
  OR if I just power off the laptop and turn it on again,
  the second screen position is set back to the default right position.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: gnome-control-center 1:3.6.3-0ubuntu53
  ProcVersionSignature: Ubuntu 3.13.0-17.37-generic 3.13.6
  Uname: Linux 3.13.0-17-generic x86_64
  ApportVersion: 2.13.3-0ubuntu1
  Architecture: amd64
  CurrentDesktop: GNOME
  Date: Fri Mar 14 08:50:00 2014
  InstallationDate: Installed on 2014-03-01 (12 days ago)
  InstallationMedia: Ubuntu-GNOME 14.04 "Trusty Tahr" - Alpha amd64 (20140226)
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=fr_FR.UTF-8
   SHELL=/bin/bash
  SourcePackage: gnome-control-center
  UpgradeStatus: No upgrade log present (probably fresh install)
  usr_lib_gnome-control-center: deja-dup 29.5-0ubuntu2

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