One of my colleagues had this issue when he upgraded from Windows 2003 DC to Windows 2008 R2 DCs:
The DNS queries to other DNS servers configured as a Forwarders sometimes timeout on the Windows 2008 R2 DCs, although it never timed out on the Windows 2003 DCs on the same domain/network.
There was no connectivity issues at all, what we found out this problem happens because of the Extension Mechanisms for DNS (EDNS0) functionality that is supported in Windows Server 2008 R2 DNS and is enabled by default.
To disable it, you can run this command: dnscmd /config /EnableEDNSProbes 0
This was fantastic. We have been struggling with the DNS to work for almost a full day. WE just ran this command and phew it worked like miracle. Thanks a bunch.
You are awesome... This instantly corrected the DNS Timeouts our clients were receiving. Thanks a bunch!