I have had an issue with DNS server in Windows 2003 server previously that’s covered pretty well in this article by my buddy Marcus. The short version is that EDNS is enabled by default on 2003 server, and this doesn’t play well with the rest of the internet, so it’s best to turn it off if you are using windows 2003 for external (internet) DNS.
Right now I’m working on a Windows 2008 R2 server and was having similar problems that made me check for EDNS many moons ago on 2003 server. This link came up in a search and it says that they made EDNS off in 2008 RTM, but it’s back on again in R2. He includes a link to Microsoft’s KB article about EDNS.
Luckily this is pretty easy to turn off. All you do is run this command:
dnscmd /config /enableednsprobes 0
I wanted to update this post with a link to a cool tool I have been using. It’s called name bench and it’s a DNS benchmarking tool. Works good, does exactly what you want, and the price is right.