How is your AD System Group Discovery setup?
If neither the AD System or System Group Discoveries LDAP strings envelop the OU or parent OU, I believe you will have a problem.
system OU name is directly discovered by AD System Group Discovery if I'm not mistaken.
I would check the adsysdis.log and adsysgrp.log on the site system supporting the clients. Run a search for the name of the OU where the clients should reside. If that OU is missing, this reinforces that the OU is not being discovered.