After the transition to Exchange Server 2010 the Exchange Best Practices Analyzer will report a critical error of “Unrecognized Exchange signature”.
ExBPA may report the unrecognized signature as 12639. The error may lead you to believe that the Active Directory Schema has not been properly prepared for Exchange Server 2010.
Unfortunately Microsoft Technet has contradictory advice on this error.
The Exchange Server 2010 planning and deployment documentation stats that 12640 is the correct schema version for Exchange 2010 RTM.
The objectVersion property is in the CN=, CN=Microsoft Exchange,CN=Services,CN=Configuration,DC= container. The objectVersion value for Exchange 2010 RTM is 12640.
However the ExBPA documentation says that 12639 is the correct schema version for Exchange 2010 RTM.
For Exchange Server 2010, the objectVersion value is 12639
As it turns out the error is the result of a bug in ExBPA, according to Jetze Mellema (an MVP).
I just received feedback from the ExBPA team, this is a known issue now and will be fixed in SP1 for Exchange 2010.
So the error can be ignored and will be fixed with Service Pack 1. Beta testers of SP1 are already saying that the problem no longer occurs in that build of the ExBPA. It would be useful to backport the fix to the current ExBPA version, and shouldn’t be all that difficult considering the ExBPA has its own builtin update feature, but it seems we just need to wait instead.