DomainDnsZones and ForestDnsZones not showing up

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I have three domain controllers, 2 server 2003, 1 server 2000. The two server 2003 machines replaced the old domain controllers which both ran server 2000, and eventually will be the only two domain controllers in the domain. The problem is that the server 2003 machines got their dns zones from Active Directory and do not have the DomainDnsZones and ForestDnsZones partitions. I have ran netdiag /fix to try to get these partitions to show up, but no luck yet. Does anyone know how to manually force the 2003 server to create the partitions? There is an option when you right click on the server in dns management "create default application directory partitions", but I am not sure exactly what it does...
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