Eu finalmente descobri que o problema estava no PDC. Eu encontrei esta entrada de log nos logs do DFSR
The DFS Replication service stopped replication on volume C:. This occurs when a DFSR JET database is not shut down cleanly and Auto Recovery is disabled. To resolve this issue, back up the files in the affected replicated folders, and then use the ResumeReplication WMI method to resume replication.
Additional Information:
Volume: C:
GUID: 89131A39-4A90-11E2-93EB-806E6F6E6963
Recovery Steps
1. Back up the files in all replicated folders on the volume. Failure to do so may result in data loss due to unexpected conflict resolution during the recovery of the replicated folders.
2. To resume the replication for this volume, use the WMI method ResumeReplication of the DfsrVolumeConfig class. For example, from an elevated command prompt, type the following command:
wmic /namespace:\root\microsoftdfs path dfsrVolumeConfig where volumeGuid="89131A39-4A90-11E2-93EB-806E6F6E6963" call ResumeReplication
For more information, see http://support.microsoft.com/kb/2663685.
Eu executei o comando, reiniciei o DFSR e a replicação finalmente entrou em ação.