All checked out fine from the Server except host -t SRV _gc....it relayed a host not found: 3(NXDomain) Is this a Global Catalog error relayed from the Windows domain?
Yes
... I wonder how this would effect the Xserve, all AD users can log into the machines my only problem is in pulling AD groups into OD. The Xserve OD DNS structure is seperate from AD, but I do have the Xserve bound to AD, I have unbound and rebound my macmini before I made the post to see if that would change anything but it did not, I think I will try the Xserve next.
Why is DNS independent? Not that it is related, but maintaining two DNS identities is going to lead to confusion at best and disaster at worst. If the primary domain is AD, you should be using only the AD DNS. In a normal AD promotion all the SRV records get created by default. While it is possible to create the service records for AD on OS X, it is usually not recommended. Too much management. My gut is to track down the absence of the GC service record. If you truly have independent DNS hosted on OS X and that is the primary resolver for the machine (assuming same domain), then try creating the svr record on OS X for the GC. Seems a bit odd but if you are at odds with the Windows admins, this might be your only way of proving that this is the issue.
You mention that users can log into machines. This is from the workstation. Have you tried dscl from the server or the workstation to see if you are able to browse the groups?