Could it be EDNS0 and because you are doing DNS queries through some
firewall?
Does the following apply:
SYMPTOMS
After you upgrade your Microsoft Windows 2000-based DNS server to Microsoft
Windows Server 2003, DNS queries to some domains may not be resolved
successfully. 
 Back to the top 

CAUSE
This issue occurs because of the Extension Mechanisms for DNS (EDNS0)
functionality that is supported in Windows Server 2003 DNS. 

ENDS0 permits the use of larger User Datagram Protocol (UDP) packet sizes.
However, some firewall programs may not permit UDP packets that are larger
than 512 bytes. As a result, these DNS packets may be blocked by the
firewall.

See http://support.microsoft.com/kb/832223 (Some DNS Name Queries Are
Unsuccessful After You Upgrade Your DNS Server to Windows Server 2003)

To modify EDNS0 configuration:
http://www.microsoft.com/technet/prodtechnol/windowsserver2003/library/Serve
rHelp/4d90d400-dc49-4772-a679-917c80096a29.mspx 



If not, enable "Debug logging" on the DNS server. The following articles can
help you with that.
* Select and enable debug logging options on the DNS server
(http://www.microsoft.com/technet/prodtechnol/windowsserver2003/library/Serv
erHelp/9b82dd18-e7b2-4c36-b981-471b7b762c46.mspx)
* Using server debug logging options
(http://www.microsoft.com/technet/prodtechnol/windowsserver2003/library/Serv
erHelp/2a2723c5-3462-411d-94e2-fe5fc08db07b.mspx)
* Debug Logging for DNS in Windows 2003
(http://computerperformance.co.uk/w2k3/services/DNS_debug_logging.htm)

Are there Event Viewer entries on the DNS server that can tell you more?

Cheers
Jorge

-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Rimmerman, Russ
Sent: vrijdag 1 april 2005 16:37
To: [email protected]
Subject: [ActiveDir] Win 2003 DNS issues


We're experiencing intermittent DNS outages ever since we upgraded our
domain controllers (which are all running DNS) to Windows 2003.  We know
we're having a problem because users see "Applying security settings"
for an extended length of time when booting up.  Then if we do nslookups on
the DNS server having issue, it times out.  If we restart DNS, it works
fine.

We applied hotfix KB830381 and thought it fixed it because it didn't happen
for awhile, but it happened again finally.  Has anyone else been
experiencing this?


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