This is an issue if you are running DFSR and using TSM as a backup client, that TSM will not backup the replicated folders. Apparently DFSR sets up the keys in
and the TSM client honours these values and would exclude replicated folders from its backup.
There is an interim fix from TSM that should fix this issue.
The manual workaround is to stop DFSR before backup runs and start it after the backup is complete.