Sorry for some of the responses in my original post, you have advanced knowledge and I missed some of your solutions already tried.
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on the X64 it is 2003 x64, it is pointing to the same as above with the old dns server as the primamy, it self as the secondary, and the parent domains DNS server as a 3rd.
In the case of installing the child domain, you need to have the primary controller for the child domain listed first for DNS resolution. Otherwise, you have a domain with no primary DNS controller for name resolution. You can then list either the Primary or Secondary DNS server for the primary domain as a backup in case the child DNS server is unreachable.
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could you be a bit more specific on ..."How is your DNS setup on the original machine?"
I have the older 32 bit set up in the primary zone, pointing to itself as the DNS server, added the new one as a second dns, then a third one from the parent domain to us.
Since you have two separate domains, a parent and a child, you need to make sure that you replicate the DNS records for each to each - otherwise they cant support each other:
Example:
Parent domain = foo.com
Child of the parent = operations.foo.com
DNS Server for parent = ParentDNS
DNS Server for child = ChildDNS
You have to make ParentDNS and ChildDNS the authoritative servers for DNS in their respective domains, and you have to add the child domain to the ParentDNS record and the parent domain to the ChildDNS record. Otherwise it doesn't matter how many computers you have tied to any domain - each domain will only be able to answer for itself.
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I have noticed some workstations pulling from one or the other, then not recieving proper group policy. e.g. I put a policy in place and some machines are not recieving the the change while others are.
Replicate the policy changes to the child domain. Group policy is domain specific and belongs on the Domain Controller for each domain. You can have one policy for the parent and one for the child, but a child will not pull policy from the parent unless inherited.
Add the appropriate scope records for the Foward Lookup (i.e: Host, DNS, WINS, etc) and worry only about hostnames and IP addresses in the Reverse Lookup...
Hope this helps.