Since you've been able to create the replica, this suggests that all feature classes/tables in the parent geodatabase has GlobalIDs and they are registered as versioned. Layers that are not versioned and/or do not have Globalids are not included in the replica.
I also wanted to check if the data being replicated is a Cadastral (Parcel) Fabric and which version of ArcGIS Desktop version (10.0 or 10.1) is being used to create the replica.
Thanks