I'm beginning to think this is an issue with your system and that for some reason it won't let Pd update or read from the registry, though I don't actually know how that would happen. If you want to see if the registry does have Pd's preferences in it, goto Start->Run, type in "regedit" and click OK. Regedit should open. In the left pane there is a folder tree; open up My Computer -> HKEY_LOCAL_MACHINE -> SOFTWARE -> Pd. In the right pane you should see something similar to the attached image (not all of it fit in the widow). If not, then it's obviously not getting updated.
That's how to do it in XP, anyway, but I think it's similar on Vista.
Please note that I am NOT asking you to update the registry, as I am definitely not an authority on it. But if you know what you're doing this is where you can bring in the pd-settings.reg file manually.
Other than that, I really can't think of anything else that could be the problem. You might want to bring this up on the Pd-list.
http://www.pdpatchrepo.info/hurleur/pdregistry.jpg