Try removing all but the main monitor, then uninstall them all
in Device Mangler.
Add in one monitor (I'd suggest the Display Port one), let it be identified and installed, then reboot and see if the settings hold.
If you are still good with two monitors, add in the third one, let it be identified and installed, then reboot and see if the settings hold.
For what it's worth, my housemate experienced three-monitor weirdness with the latest ATI driver
. (As of two weeks ago - they move pretty fast these days...) She never had any trouble before that.
I also have three monitors, and though I didn't have any trouble after I loaded the new video driver I did have to re-sort them all out after the first post-install reboot.