If you have separate DNS servers operating here, then you should have your Mac OS X Server box "aimed" at those for DNS name resolution; you should likely not be running (another) DNS Server locally on your Mac OS X Server box. Just configure the standard DNS forwarding on your NICs and aimed at your production DNS Server(s) running on the other box(es) on your network.
And if your dedicated DNS Server boxes are not correctly configured and regardless of the host platform underneath your DNS Server(s), then you can and often will have network issues.
DNS must be configured, and DNS must work, and DNS errors must be resolved.
This irregardless of whether you are running the client or server versions of Mac OS X Tiger, Leopard or Snow Leopard, or running Windows or Windows Server, or OpenVMS, Tru64 Unix, Linux, BSD, Solaris, [insert your other preferred OS here] or any other operating system.
DNS is fundamental to correct IP network operations.