There are no known issues or bugs with UBDR changing security ID's. If you had a drive failure, it is possible that the backup itself was affected by the cause of the system failure.
Windows running the chkdsk is the result of UBDR writing the data back exactly the way it was when the volume was backed up. I have seen this in the past and there is nothing that can be done except trying to restore an older backup that hopefully is not affected by the same issue.
Technical Support Manager