In 6.1, katello-agent from Satellite 6.0 is not compatible. This means that all capsules must be upgraded to 6.1 before attempting to synchronize any repositories. Unfortunately, this also means Satellite clients need to be *manually* upgraded to the new version of katello-agent, perhaps via SSH'ing into the server.
Since this issue was entered in Red Hat Bugzilla, the release flag has been set to ? to ensure that it is properly evaluated for this release.