I'm running a domain with two DCs, one is 2008 and the other 2003. The delay in replication between the two is frustrating enough to begin with, but I've noticed that even days after a change is made, the new settings only affect half the office. What's worse, it switches halves!
I first noticed this by setting a wallpaper image for everyone in a group. The image was stored in a very public directory, but only half the office got it. Half an hour later, those people didn't have it but the other half did.
Last Friday I installed sysinternals bginfo on every workstation in the office, and used the 2008 DC's Preferences to push out a registry key to all users, to stop the program from displaying the EULA. I included the logon server in the wallpaper configuration. As I started installing, initially none of the computers got the new key. Then only those connected to the 2008 DC. About 2/3 of the way through, I noticed the 2003 DC was handing out the key, but now the 2008 wasn't.
It's almost as though there were only one valid copy of the policy, and the servers were handing it back and forth periodically.
I know enough about group policy to deploy new settings and troubleshoot problems caused by OU linking and application order, but domain replication gets over my head fast. I'm hoping someone recognizes these symptoms and can point me in the right direction!
In case it matters, I'm using mandatory roaming profiles (renaming with .man). I've eliminated them as the culprit by creating a new standard roaming profile, which encountered the same problems.