I’ll take a stab it this one…It sounds like your running an AD domain in native mode with a functioning Exchange 5.5 server in the mix. Since the Exchange 5.5 server is not AD compliant, your new Exchange 2003 server is not recognizing it as a peer.
Try taking your new Exchange server off line so as not to confuse things, and upgrade your existing 5.5 server to Exchange 2003. Remember you’ll need to upgrade the server OS from 2000 to 2003 as well. Exchange 2003 does not play well with Server 2000. Once you’ve completed the upgrade and tested your box, add your new Exchange 2003 server in domain1 to the organization. You should be able to see the server in domain2 now and proceed with your migration.