I see your other post, with the single DHCP server servicing clients from your 2 domains. My sense is that something is flaky with your DNS. The first DNS server that your DHCP server hands out, does it have BOTH domains listed in its forward lookup zones, and are both zones fully populated? I'm guessing no.
Whichever domain the first DNS server is NOT a member of, will have to be loaded into the active (first-listed) DNS server as a SECONDARY zone. In order to do this, you will have to manually add this server's as a NAMESERVER for the zone so that it will be allowed to transfer the zone data, and allow zone transfers to all nameservers. You do this in the DNS properties of the zone.
Or if the first-listed DNS server is Server 2003, you can specify a FORWARDER for the other domain pointing to the DNS server for that domain.
You'll also want to populate the DNS suffix list in DHCP with BOTH domains.
Confusing I know, but if you can't follow along, post back, or perhaps someone else can clarify.