We have recently moved all of our domain controllers to Server 2008 R2. As a result they all run DNS server and for the most part work correctly. On the last one we installed (which also holds all the FSMO roles) we are having some issues with the DNS service randomly giving up.
When it fails it will no longer resolve queries for most external domains, however not all. Internal hosts all resolve correctly. I am not using forwarders on any of the servers, only root hints. Under monitoring both simple and recursive checks pass. There is nothing obvious logged in event viewer or showing up in the debug logging.
When we first started using 2008 R2 DNS we had issues with EDNS causing this kind of behaviour, however it has subsequently been disabled on all DNS servers.
Now at a loss, any suggestions greatly appreciated!