I never did really thought on how to run more than one Domain in the same network. I had always separated the networks thru the physical media. As pointed out DHCP will register automatically with DNS. I also hear in one webcast 2 weeks ago, that on multiple domains (here becomes kind of fuzzy my memory) even thought you are registered with one domain, if you are getting settings from another, it will try to talk with the other bla bla bla. Sorry, I can't remember well, but it should provide some area to think. I would say, Check which GC you are connecting too. Check the DNS settings in the DNS server. (from the DNS console and the network properties) Make sure it is pointing to itself, and that it has forwarders set up. Check the partners replication (you don't want it to synch with other domain DNS)(thought then again, in some cases you might want to)
I find it a lot easier, to make a list of which server should have which service, and then I check to make sure those settings are true