Perhaps this can be fixed by changing the properties of the Nvidia configuration tool to add the "sudo" command.
Go to system>>preferences>>main menu and search for the Nvidia settings under Administration (or preferences, as apparently there's one there too now). Go to properties after selecting this, and change the command to "gksudo /usr/bin/nvidia-settings." This will give you a prompt to enter the root password so that you can modify Xorg.conf. Otherwise, nvidia-settings will not have permission to alter the file (unless you are logged in as "root."
I hope that helps.