We were having some weird DNS issues recently with our DNS servers at work. We recently upgrade one of our internal domain controllers with Active Directory-integrated DNS services to Windows Server 2008 R2. After the upgrade we found that DNS queries for some hosts did not resolve while others worked just fine. Another domain controller running non-R2 Windows Server 2008 would resolve the queries just fine.
One of our network engineers stumbled across a Microsoft KB article describing our exact problem:
