I ran the Exchange 2010 BPA today to see if it picked up any problems. It picked up only 1 critical problem which was the following error:
Unrecognized Exchange Signature: Active Directory domain ‘XXXXX’ has an unrecognized Exchange signature. Current DomainPrep version: 12639
Went to MSDN to check that my domainprep version was valid but I am running at 2008 R2 Domain Functional Level.
This is a bug in the Exchange 2010 Best Practice Analyzer. It will be resolved in Exchange 2010 SP1.