Having set up a Server 2003 Domain Controller in a remote site we found the following error whilst trying to replicate between the two locations, Active Directory and DNS seemed to replicate correctly however the Sysvol folder remained empty, the error is below:
Event ID: 13508
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.
 FRS can not correctly resolve the DNS name from this computer.
 FRS is not running on .
 The topology information in the Active Directory for this replica has not yet replicated to all the Domain Controllers.
This event log message will appear once per connection, After the problem is fixed you will see another event log message indicating that the connection has been established.
In our case it was a firewall between the sites blocking the RPC traffic so once this was opened up between the two servers it replicated without any problems. Here’s the article we found on Experts Exchange that helped us go through the quick checks:
1) Examine the FRS event ID 13508 to determine the machine that FRS has been unable to communicate with.
2) Determine whether the remote machine is working properly, and verify that FRS is running on it. Type the following command at a command prompt on the computer that logged the FRS event ID 13508 and press ENTER:
If this fails, check network connectivity by using the Ping command to ping the fully qualified domain name (FQDN) of the remote domain controller from the computer that logged the FRS event ID 13508. If this fails, then troubleshoot as a DNS or TCP/IP issue. If it succeeds, confirm that the FRS service is started on the remote domain controller.
3) Determine whether FRS has ever been able to communicate with the remote computer by looking for FRS event ID 13509 in the event log and see if the FRS problem correlates to recent change management to networking, firewalls, DNS configuration, or Active Directory infrastructure.
4) Determine whether anything between the two machines is capable of blocking RPC traffic, such as a firewall or router.
5) Confirm that Active Directory replication is working. For more information about troubleshooting Active Directory replication, see Troubleshooting Active Directory Replication Problems in this guide.
Having gone through several articles we also found alot of users fixed this via a registry tweak. It’s a D2 tweak on the ‘secondary’ server telling it to pull replication from the Primary DC and a D4 registry tweak on the ‘primary’ server telling it that it holds all of the master records to replicate out.
D2 – Non-Authoritative restore (pull from another DC)
D4 – Authoritative restore
Steps for setting D2/D4 are:
1) Stop File Replication service via Start – Run – type in CMD, click ok. In the Command Prompt window type ‘net stop ntfrs’ and press enter
2) Use RegEdit to edit “BurFlags” in the key “HKLM\System\CurrentControlSet\Services\Ntfrs\Parameters\Backup/Restore\Process at Startup”
* edit the dword key “BurFlags” in Hex format.
* change from 0 to D2 or D4
3) Start the File Replication service via Start – Run – type in CMD, click ok. In the Command Prompt window type ‘net start ntfrs’ and press enter