I paused the project and shut down FAH before starting the reconfig, on startup however the project started all over again

Anything I (or any of you) can do about this or did I just waste quite some time and a couple of points?
p.s. don't understand a thing about the qfix thingy but i can send the FAH log files if needed (it seems to have the old one stored in C:\Documents and Settings\*Username*\Application Data\Folding@home-x86 and the one it's working on now in just C:\Documents and Settings\*Username*. Is it possible to start the file from app data instead of the current location?
They both still have the same project code strangely.
-update: fixed it by copying the files to C:\Program Files\Folding@home\Folding@home-x86 and start FAH from there (I accedentically ran accross it when I started FAH from that folder, saw it made the same files as stored in app data and Docs & Sets