I just received feedback from the Dev Team that an updated version of DirSync Tool has been released that fixes the below Exception in Windows 2003 Domain Controller environments.
Microsoft.Online.PasswordSynchronization.DirectoryReplicationServices.DrsException: RPC Error 8440 : The naming context specified for this replication operation is invalid. There was an error calling _IDL_DRSGetNCChanges.
Grab the updated tool in the Admin Portal - version number is 6411.0007.
I can confirm that this version fixed the above issue in my environment.