That is perfectly normal. Windows 2000 DC MUST take role of PDC (emulator)
Another tip is when you install a second DC to keep your BDC for emergency needs aside. Take it off the network and keep in a safe place, so you're always able to rollback.
Blutch
PS Don't understand your question actually, you say "when I install my first 2000 server in my existing domain, and then validated in my new ???