Nvidia driver fails to save primary display

[LostMyOtherAccount]

I have two monitors (same model) and want the left one to be the primary monitor. When I make the setting in the nvidia settings tool it works as it should, but after a reboot the right monitor is primary again. It doesn't matter if I merge the xorg.conf or just overwrite it, neither works.

ProblemType: Bug
DistroRelease: Ubuntu 12.04
Package: nvidia-common 1:0.2.44.2 [modified: var/lib/nvidia-common/last_gfx_boot]
ProcVersionSignature: Ubuntu 3.2.0-49.75-generic 3.2.46
Uname: Linux 3.2.0-49-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 2.0.1-0ubuntu17.3
Architecture: amd64
Date: Thu Jul 25 09:21:59 2013
InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Beta amd64 (20120301)
MarkForUpload: True
ProcEnviron:
 PATH=(custom, no user)
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: nvidia-common
UpgradeStatus: No upgrade log present (probably fresh install)

[LostMyOtherAccount (rocketscienc01100101)]

The workaround for this is to use the Ubuntu config tool in System Settings -> Displays. Drag the menu to the screen you want to be the main screen and it will be saved across sessions.