I have at least one install go south on me where the DB on the sub came out of sync. Phones would not register, MOH, etc. Ended up having to rebuild the sub completely. If you can, start up the RTMT and check the logs to see you are having DBreplication errors. If you are, this is why.
Another item to check is your CallManager Group. If you did not add the subscriber to the CUCM group, then all phones will be on the sub.