Ah, it's the "x" option sent to rsync, sorry about overlooking that. The x tells rsync not to cross file system boundaries. You can either:
- Run the script separately for each mount point that's on a different file system (/, /home, /var, /usr, and if you're being thorough, /boot and /tmp), or
- You can edit line 531 of the script, where it defines the rsync arguments. If you edit the arguments, just take the "x" out of the string and you should be able to copy / and get everything migrated.