Primary screen forced to left after reboot (Gnome on Trusty Tahr)

I have a dual screen set up where I need the primary screen to be the one on the right. I can achieve this with the "Screen Display" settings dialog but after reboot the primary screen is forced to the left resulting in the mouse having to scroll off the right of my right hand display to get to the screen on the left. If I have the primary monitor being the one on the left then there are no issues after reboot.

This is what is in the ~/.config/monitor.xml

<monitors version="1">
  <configuration>
      <clone>no</clone>
      <output name="DVI-I-0">
      </output>
      <output name="VGA-0">
      </output>
      <output name="DVI-I-1">
          <vendor>VSC</vendor>
          <product>0x0f1c</product>
          <serial>0x01010101</serial>
          <width>1280</width>
          <height>1024</height>
          <rate>60</rate>
          <x>0</x>
          <y>0</y>
          <rotation>normal</rotation>
          <reflect_x>no</reflect_x>
          <reflect_y>no</reflect_y>
          <primary>no</primary>
      </output>
      <output name="HDMI-0">
          <vendor>IVM</vendor>
          <product>0x6107</product>
          <serial>0x01010101</serial>
          <width>1920</width>
          <height>1080</height>
          <rate>60</rate>
          <x>1280</x>
          <y>0</y>
          <rotation>normal</rotation>
          <reflect_x>no</reflect_x>
          <reflect_y>no</reflect_y>
          <primary>yes</primary>
      </output>
      <output name="DVI-I-2">
      </output>
  </configuration>
</monitors>

Some details on my set up:
Ubuntu version:
  Description: Ubuntu 14.04 LTS
  Release: 14.04
Graphics card: nvidia GeForce GTX 460
lspci: 03:00.0 VGA compatible controller: NVIDIA Corporation GF104 [GeForce GTX 460] (rev a1)
Driver used: nvidia binary driver version 331.38
Left screen connected by DVI
Right sceen connected by HDMI
xorg.conf - do not have one

I have tried removing the monitor.xml and using the nvidia-settings to set the right screen as primary but this setting does not survive reboot, even after saving to an xorg.conf