I recently migrated 2 DNS servers from Windows 2003 to Windows 2008R2. Now, I have an odd situation where all the secondary zones on the second server show "Zone never loaded" on the general tab of their properties. Both servers are Windows 2008R2 and all the zones are not AD-integrated and are set to load from file at service start. I can successfully run nslookup and perform an "ls -d zonename.com" from each server to the other, so I know zone transfers are properly configured and working. I can also query for records remotely and changes to the primary are updated in the secondary zones. If I delete the secondary zones and re-add them, the Status on the zones is "Running". But, as soon as the DNS service is stopped and started back up, the status goes back to displaying "Zone never loaded". I can then right-click the zone and select "Transfer new copy of zone from Master", then the zone goes back to displaying "Running" until the DNS service is stopped and started again.
Is this the intended functionality in Windows 2008R2 DNS server? It did not work this way in Windows 2003 DNS server, as the secondary zones showed "Running" all the time.