I did a backup from one server and restore on another using SME5.6, and none of my /cgi-bin scripts would run. Turns out none of the permissions were set to the same as the original and I ended up doing a RSYNC to recopy the files and permissions - it was faster than changing all of them manually.
I see there is a newer backup utility available for SME6.0... does it address the file permission problems?
Wes