Is this Hibernate 3.2.0.GA? Just so you know, some CRs had a bug in the way Fqns were generated by Hibernate, and everything ended up as direct descendents of Fqn.ROOT.
Thanks very much. That's exactly what the problem was. Turns out I was using Hibernate 3.2.0CR1 ! Switching to 3.2.0GA fixed it.
Thanks for your help!