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I've got a couple Server 2008 R2 boxes that are doing DNS resolution, and I'm finding that a specific URL is not resolving through either one of them. I can use nslookup from both to connect to the authoritative name servers and request the records manually, but the DNS services can't resolve the addresses. Any ideas on how I could troubleshoot that?

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Are you using root hints or forwarders for Internet bound DNS requests? – Solignis Mar 23 '11 at 19:04
DNS servers don't resolve URL's. Can you give us the specifics on what's not resolving? – joeqwerty Mar 23 '11 at 19:07
The servers are using root hints for resolving. – MikeSmitty Mar 23 '11 at 19:22
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3 Answers

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Use Wireshark to watch the DNS Server trying to recurse the hostname.

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I'm watching the traffic on Wireshark, but unfortunately there is a good amount of traffic going in and out so it's taking a bit of work to separate the DNS traffic. – MikeSmitty Mar 23 '11 at 19:23
Filtering it to port 53 should help. See the Wireshark Wiki on DNS for more info. – Chris S♦ Mar 23 '11 at 19:30
Looks like it's getting a Format Error response from one of the authoritative DNS servers. – MikeSmitty Mar 23 '11 at 19:37
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Checking the event logs there were a ton of 5504 events. Using the instructions I found on this page I was able to fix the resolution: social.technet.microsoft.com/Forums/en-US/winserverPN/thread/… dnscmd /config /enableednsprobes 0 – MikeSmitty Mar 23 '11 at 19:46
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You can filter the DNS traffic in wireshark using "(dns)".

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verify that the fowarders and root hints are configured properly. Since you can connect from the server to the authoritative NS it means that the DNS server is not querying properly recursively. See How DNS query works

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