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SuperDuper! does not change the source drive, Jon -- and if you selected "Repair Permissions", as I said before, we ask Disk Utility to do it, and it does what it does.
I don't know why it's not repairing Library. But the "@" means there are EAs attached, likely a deny-delete ACL. You can see the ACLs by using the "@" option w/ls.
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--Dave Nanian
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