I ran the Exchange 2010 Best Practice Analyzer in my test lab 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 ‘TESTLAB’ has an unrecognized Exchange signature. Current DomainPrep version: 12639
Hmmmmmmm ok. So i went off to MSDN to check that my domainprep version was valid, and indeed it was. I am running at 2008 R2 Domain Functional Level.
As it turns out this is a bug in the Exchange 2010 Best Practice Analyzer. It will be resolved when Exchange 2010 SP1 will be released later in the year.