After a bit of research it transpired that the group policy management console tries to connect to the PDC when working with group policies. I tried browsing to my SYSVOL share on the new domain controller and low and behold it was not there! As you can imagine this concerned me greatly. The first place to check was the File Replication Service log in the Event Viewer of both servers. The older of the two domain controllers log was full of Errors with Event ID: 13568
The File Replication Service has detected that the replica set "DOMAIN SYSTEM VOLUME (SYSVOL SHARE)" is in JRNL_WRAP_ERROR....
This error had been present for more than two years. The second server's log was full of Event ID: 13508 warnings
The File Replication Service is having trouble enabling replication from
to for using the DNS name . FRS will keep retrying.
Following are some of the reasons you would see this warning......
This seemed like more of a generic error and so I suspected my fault lied with the first server. I tried restarting the netlogon and ntfrs services as a first resort but the problem still remained. A bit of Googling later and I came across this Microsoft article which sounded like it could be of help.
After reading the article I stopped the ntfrs service on both servers and navigated to the HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\NtFrs\Parameters\Backup/Restore\Process at Startup registry key. I only had one copy of the SYSVOL directory and so had to be careful to get the next step the right way round, otherwise I would be restoring from backup. On the first server I modified the BurFlags DWORD value to D4 which means do an authoritative restore and on the second server I modified Burflags to D2 which means do a non-authoritative restore.
I started the ntfrs service on the first server and then on the second server. Voila the SYSVOL directory was now replicated and the netlogon service was automatically notified, which in turn shared the SYSVOL directory out. I opened the group policy management console and the network errors were no longer present. A 5 minute group policy change had turned into a nerve racking couple of hours research and fault fixing! However, I am now a wiser man and I hope somebody else will be able to make use of this blog one day.