Does the Windows 2003 server update its dns-record in the AD/DNS?
If not, what happends if you set a static A-record in the DNS pointing to the server? That should make the name-resolution work since it has nothing todo with the actual server itself.
Are you using ipv4 or ipv6? If ipv4 try to disable the ipv6 since this are sometimes causing some issues.
// Linjo