Windows 2000 DNs Disjoint namespace

Recently upgraded a PDC to Windows 2000. All seamed to work well until I went to upgrade a BDC. Active directory will nut run on the BDC, can not find the dc etc.

If I turn off the Upgraded DC, there is no authentication, even with 2 other BDC’s on the network.

Background info:
All servers point to a unix dns box.
In NT4 the dns domain name we used was not our true domain name.
Windows 2000 DC still points to Unix DNS
It appears that DNS did not fully install on the DC