List of Root Hints Empty Windows Server 2008 DNS

If you have local DNS names (which you do), generally you'd want to set your DNS and AD server to use only itself as a DNS server. You want all your other servers and client workstations to do the same. It's the closest thing to you, and public DNS servers don't carry your local domains. The standard doesn't require that a DNS client try each resolver it has if one of them returns a SERVFAIL or NEXIST, and in fact most don't. The actual behaviour is that they either use all the DNS resolvers configured in round-robin, or only move down the list if the primary one is not reachable.

Resolving DNS names using root hints is never a bad idea; it removes one point of failure (the forwarders, which may change or go down). If you can't, at least prune the forwarder list frequently.

Ablue, these are my observations:

Query packet 161 - quad A query dc2 - response packet 162 - server failure.
Query packet 251 - quad A query mx1 - response packet 252 - server failure.
Query packet 2102 - quad A query for Storage1 - response packet 2103 - server failure

Gaps:

Successful response from external DNS ends at Jun 1, 2012 08:40:07 with packet 3913

Queries go out to external servers.
DNS caching server does try multiple servers from forwarders,
but does not receive a response from external servers.

Next response from external server received at Jun 1, 2012 08:40:46 with packet 4147

packet 4147 - packet 4453

4504 - 4600 - 4694
4869 - 5004
5210 - 5234

By looking at these gaps out of your pcap file I can see that your DNS server is going out to the forwarders. However, it is not receiving responses from the forwarders. Have you checked if you had connectivity issues at or beyond your border router/gateway? You seem to be experiencing line dropouts.

By what the timestamps in the packets tell, it's also during the morning rush hour.