There is a script that rewrites the settings if it detects a change. I haven't found it or how to defeat it but I have managed to change the settings andget them to stick. But I'm not sure what I did that actually did it.
Either editing after killing x (from a terminal run init 3 or you can run /usr/pluto/bin/Stop_X.sh) or ssh in from a remote terminal using Putty (log into the core, sudo su, ssh (MD's IP address) and edit the xorg.conf. But I'm not sure which.