Don't know what to tell ya
If it were a perms issue, then chown would have fixed it.
BTW, you don't need all those switches. Just use -ar with an optional v
If you're indicating that this is a result of the upgrade, you're mistaken. This isn't a result of the upgrade, it's a result of not getting a full backup.
Considering I wrote the original backup and restore procedure for the Open Source Edition, I'm sure it works.
Sorry. If you find out any more, please do let us know. We're here to help
Good luck