I am running Kubuntu 12.10. I have 3 monitors plugged into a AMD Radeon 7970. I have tried switching the order of the outputs, and configuring them repeatedly with amdcccle but kubuntu always seems to make the farthest monitor on the left the primary monitor. The solution so far has been to do the following.
Which returns a list of my monitors. Then explicitly setting the primary with xrandr with
xrandr --output <monitor identifier> --primary
I added this command to a start up script, but it still seems hacky. The system still boots with the left most monitor as primary, and then switch to my centre monitor after startup. Several of my applications still treat the left monitor as primary and will launch there instead of on the monitor I want as primary.