Question: Why won't OCS 2007 start after we've updated to OCS 2007 R2?

Answer: In February/March 2009 Microsoft Released OCS 2007 R2, with it they incorporated a certificate limitation with the Response Group Service where the pool FQDN would have to be the last SAN entry.

Microsoft Office Communication Server 2007 R2 Release Notes:

Certificate Limitation With Response Group Service
Issue: If the certificate assigned to the Office Communications Server 2007 R2 or to the Office Communications Server 2007 R2 Web Components Server contains a SAN list, the pool FQDN must be the last entry.

Resolution: Move the pool FQDN to the last position of the SAN list.

Solution: Microsoft released a Hotfix in March/April 2009 that removes this limitation. KB967829