I seriously doubt that the per server vs per seat is an issue unless you are getting licensing errors in the event log. DNS is a more likely suspect.
You did not mention whether this was an upgrade from NT 4.0 or a new AD installation. If you upgraded, you may want to make sure that the Domain Controllers FQDN is properly set. Run IPCONFIG /ALL to see the information. If the Domain Controllers FQDN (listed at the top of the IPCONFIG display) does not match the domain name, then you have a problem that will require a rebuild of the AD. Here is what I mean:
Let's say I upgraded my NT 4.0 PDC to a Windows 2000 machine. Originally my DNS suffix on NT 4.0 was .Domain.com so my DC was called MYDC.Domain.com. When I create the AD, I decided to call my domain MYDomain.com. Since I did not change the NT 4.0's DNS suffix prior to the upgrade, I end up with this:
FQDN of Server = MyDC.domain.com
FQDN of DOmain = My.domain.com
These are incompatible, resulting in an inability for the DC to locate itself and it's domain resources correctly. Rebuilding of the machine is required. Now, I am not saying this is your problem, but you will want to check. Remember, start with NETDIAG.exe (and perhaps DCDIAG.exe) to diagnose the problem.
Dig deeper on Domain Name System (DNS)
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