Have you read this entry from the Supervisor FAQ: How do I move my repository?
Based on symptoms, I’d guess that you did not. I think you are getting cross-linked repositories because I suspect you did not IMMEDIATELY go into the copied repository (once you generated the BOMAIN.key via the safe recovery) and then change ALL CONNECTIONS to point to the new server.
Anita Craig 
(BOB member since 2002-06-17)