The BPA is a pretty old tool (dated august 2008)
By default it does not recognize OCS 2007 R2 so you need to update the tool!
If you want to update this tool on Windows 2008/2008 R2 you can’t update the signature files and just says “An error occured trying to access the web”

Best Practices Analyzer for Office Communications Server 2007 and Office Communications Server 2007 R2
http://www.microsoft.com/downloads/details.aspx?FamilyID=1b90993c-072a-4c84-b385-b76d23b2f27c&displaylang=en

Only when you start the BPA with Administrator credentials then you can update it
(Yes UAC is the problem here)

Happy BPA-ing :)