Ran into a weird issue the other day. I could configure my second monitor location but whenever I restarted my server my monitors would reset back to default right and left position which I did not want. I could see both but they where set up out of order. I tried to configure the xorg.conf using Navidia-settings and confirmed that it was updated but still after ever restart my monitors defaulted back to their former locations. After a crazy day of looking around here is what I found..
To my surprise there is a file located in the user directory in ~/.config/monitor.xml which holds the duel monitor configuration. It is created in the “System settings” / “Displays” since I had been using the Nividia configuration program only to configure Navidia card I had never gone there and saved the configuration so I had no Monitor.xml file. Even though Ubuntu saw the second monitor it never keep a record of location so it always defaulted back. Just set it up using the “Display” then confirm the monitor.xml is has been created and you are good to go.