First, let me give you some information on our current setup: We have a main site and two branch offices. Two DCs are installed at our main site, and one is at each branch office. The main site and the two branch offices are each in a different subnet and in different sites on Active Directory Sites and Services.
The DCs are:
DC1 (main site, Server 2003 x86)
DC2 (main site, Server 2003 R2 x64)
DC3 (branch office 1, Server 2003 x86)
DC4 (branch office 2, Server 2008 x64)
The two branch offices are connected to the mainsite over a 10Mbit Fibre Connection. The connection is very stable and all ports are open between the sites.
DC4 is the newest DC in our setup and I've been having this problem from the moment i've ran dcpromo on DC4. I have even reinstalled DC4, but it did not change anything.
For debugging reasons i have set DC4 to replicate with all other DCs. I first tried to replicate only with one DC at our main site, but this had the very same effect. Once I reboot DC4, it will not have any INBOUND replication for roughly 12 hours. OUTBOUND replications work fine. Running repadmin /showrepl gives nothing but successes on DCs 1-3 (also replications with DC4 are reported successful), but fails miserably for every try on DC4.
repadmin /showrepl ran against DC4 gives two different errors. For DC=domain, DC=tld ; Configuration ; Schema, the error is "result 1396 (0x574): Logon Failure: The target account name is incorrect.". For DomainDnsZones and ForestDnsZones, the error is "result 1256 (0x4e8):The remote system is not available. For information about network troubleshooting, see Windows Help."
Additionally, I have a couple of errors 1311 and 1645 in Event Viewer, along with 1925 and 1566 Warnings (they pop up every 15 minutes, so I assume for every replication try).
As mentioned, this only happens for the first 12 hours after a reboot of DC4. Once this certain time (or number of retries?) has passed, all event errors / warnings stop and changed items are replicated. repadmin /showrepl shows no errors anymore and the replications works fine as far as I can tell.