Yes, we found the config file, however making it false and restarting DA resulted in nothing.
The link is still there
I take it then you're running suphp. Check the /var/log/suphp.log for clues as to why it's complaining. It's probably either the user/group or permissions of the copied files. Check the log and check to see what the permissions are.
Attached are some screenshots.. note fc6.com isn't ours, nor is it "real" in this case, it's just a fake domain on our fedora 6 box on an internal network.