You may be able to modify the UserDir="C:\MentorGraphics\9.3.1PADS\SDD_HOME\Settings" in the Powerpcb.ini file.
Not sure if it will solve your problem. Actually it may cause other problems.
I will recommend using the same method as we do in our company.
We have a script that copies all setup files from a network drive to the local computers during reboot of the computer.
It is a simple solution but works very well.
Thanks for your reply. I'll look into it when time allows.