Server 2008 R2 DNS Server Not Resolving Particular Address

If I'm not mistaken, it's determined by the NIC binding order in the Advanced Settings in the network connections folder. You can verify it by changing the binding order of the various NIC's and running nslookup as a test.

To expand on my answer, citing the article that Evan linked, here is an excerpt from said article:

The DNS Client service queries the DNS servers in the following order:

1. The DNS Client service sends the name query to the first DNS server on the preferred adapter’s list of DNS servers and waits one second for a response.

2. If the DNS Client service does not receive a response from the first DNS server within one second, it sends the name query to the first DNS servers on all adapters that are still under consideration and waits two seconds for a response.

3. If the DNS Client service does not receive a response from any DNS server within two seconds, the DNS Client service sends the query to all DNS servers on all adapters that are still under consideration and waits another two seconds for a response.

4. If the DNS Client service still does not receive a response from any DNS server, it sends the name query to all DNS servers on all adapters that are still under consideration and waits four seconds for a response.

5. If it the DNS Client service does not receive a response from any DNS server, the DNS client sends the query to all DNS servers on all adapters that are still under consideration and waits eight seconds for a response.

The preferred adapter in step 1 being the adapter that's listed first in the binding order.

Per this Microsoft KB article the solution is to change the MaxCacheTTL registry value (HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\DNS\Parameters\MaxCacheTTL) to 2 days or longer.