Keep this DNS issue in the back of your head when migrating from 2003 to 2008 R2 as Microsoft didn’t allow for backwards compatibility with EDNS. Essentially what happens is when the internal DNS box queries an external DNS source, if the packet is larger than 512 bytes or the remote DNS server doesn’t support EDNS, the query fails. EDNS was turned on by default in Server 2008 R2 which is why it was never an issue with 2003, 2003 R2 and 2008.
DNS queries failing on DNS servers that run Windows Server 2008 R2
Extension mechanisms for DNS (EDNS) are enabled by default on Windows Server 2008 R2. If you notice queries that used to work on DNS servers that run Windows 2000, Windows Server 2003, or Windows Server 2008 fail after those DNS servers are upgraded or replaced with DNS servers that run Windows Server 2008 R2 or you notice that queries that the old DNS servers can resolve cannot be resolved by Windows Server 2008 R2 DNS servers, disable EDNS by using the following command:
dnscmd /Config /EnableEDnsProbes 0
Here are a few articles to support the finding.
http://support.microsoft.com/kb/832223
http://weblogs.asp.net/owscott/archive/2009/09/15/windows-server-2008-r2-dns-issues.aspx
