Something that comes as a surprise to many Exchange administrators is that the Exchange System Management (ESM) tool does not use DSAccess to discover the DC it will talk to. Instead it discovers the DC it will use on its own, using ADSI to do a server-less binding to the directory. The reason behind this is because of ESM's extensive use of and queries to Active Directory.
This is not of any concern and normally it's not a problem. However, if you do get into the scenario where your Active Directory is out of sync and it so happens that the DC referred to your server by DSAccess does end up being different than the DC ESM has bound itself to (ESM & server in different sites for instance), you could find that settings modified are delayed being picked up by the server while waiting for replication to take place. This could also account for an apparent difference in the setting you view and what the server appears to be using, although this shouldn't happen unless you have just modified the setting or your AD replication between the DCs being used is behind.