Using the latest KDS 3.2, I started getting the above error when opening Processor Expert perspective. I also cannot create new PEx projects. I also get an error saying "Processor Expert configuration file not found or corrupted (PE[_??].cfg)."
I have KDS installed on Fedora 25. Running KDS as a different user (like root) doesn't have this error. So it seems to be specific to my user.
Any help would be appreciated, thanks.