I just checked a few files, and a couple of folders, on the site that are not in the backup. The 'admin' account (imaginatively named), the global admin, is showing as an Owner on all of them.
Let me generate the logs and see if I can find something. Do you know of a specific error message I can search for, since those things are so huge?
edit: The permissions on some of the files that were copied are identical to the ones that weren't.