Doh it stripped my example images.
Raw HTML, no domain user drive C access:
http://i284.photobucket.com/albums/ll9/DMahalko/Message%20Boards/domain-users-no-C-write-access.png
AppData redirected to file server:
http://i284.photobucket.com/albums/ll9/DMahalko/Message%20Boards/redirecting-roaming-appdata-to-file-server.png
Foldit used to store data in user space. You can still see remnants of this in the FAQ. I don't know why they changed it. Maybe to help people find the data files, or maybe to help back up their foldit installation before updating (it is beta software and updates sometimes break). Maybe they wanted to unify more of their PC/OSX/Linux code.
It bit me as well, I assumed all the user common data like the puzzles were in C:/Program Data and my work was in my Appdata…lost my first month's of folding when I bought a new hard drive and didn't back up Program Files.
Anyways, it USED to work as you describe (except for local appdata) and they changed it for some reason. You're going to have to argue against that reason. I'm sure it's causing more problems than it solved.
Listen DMahalko, he is right!