I'm also experiencing this issue.
The AD Domain Controllers are all GC servers but I still can't configure the AD plugin over the GC port using either port 3268 or 3269 (with SSL). Also can't seem to use vCO workflows to manage AD objects in child domains or do queries from any child domain, it only works with the root domain. I would have hoped by now in vCAC v6.1 that the AD plugin was capable of working with child domains by now.