Check on the Flexible Single Master Operations roles (FSMO). If the roles got switched around it could cause a problem with replication. Specifically the Infrastructure Master role should not be a Global Catalog Server. If it is, the replication can fool itself into believing that all of the child domain servers are up to date, when they are not. Keep in mind that you will have multiple Infrastructure Masters. Each domain/child domain will have its own. Unless ALL servers are Global Catalog servers -- you will need to make sure the ones running the Infrastructure Master are not be GC's. You may use the DSA to find the information or the NTDSUTIL.exe (my preference):
Open a command prompt and type Ntdsutil (this requires that the Windows Support Tools have been installed from the CD). You get a NTDSUTIL: prompt. Now type…
Ntsdutil: roles
fsmo maintenance: connections
server connections: connect to server [servername of non-PDC emulator system]
Connected to [servername] using credentials of locally logged on user.
server connections: quit
fsmo maintenance: Select operation target
select operation target: List roles for connected server
The output will be similar to this:
Server "myserver" knows about 5 roles
Schema - CN=NTDS Settings,CN=MYSERVER2,CN=Servers,CN=Default-First-Site-Name,CN=
Sites,CN=Configuration,DC=mydomain,DC=com
Domain - CN=NTDS Settings,CN=MYSERVER2,CN=Servers,CN=Default-First-Site-Name,CN=
Sites,CN=Configuration,DC=mydomain,DC=com
PDC - CN=NTDS Settings,CN=MYSERVER,CN=Servers,CN=Default-First-Site-Name,CN=Site
s,CN=Configuration,DC=mydomain,DC=com
RID - CN=NTDS Settings,CN=MYSERVER2,CN=Servers,CN=Default-First-Site-Name,CN=Sit
es,CN=Configuration,DC=mydomain,DC=com
Infrastructure - CN=NTDS Settings,CN=MYSERVER,CN=Servers,CN=Default-First-Site-N
ame,CN=Sites,CN=Configuration,DC=mydomain,DC=com
Paul Hinsberg
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