In Exchange Server 2007 RTM and SP1, the Exchange team has published guidance for using a CNAME record in DNS as part of the provisioning process for the file share witness (FSW) component of a Majority Node Set (MNS) quorum on Windows Server 2003, and a Node and Share Majority quorum on Windows Server 2008. Specifically, we state the following in the documentation:

“We also recommend that you create a CNAME record in the Domain Name System (DNS) for the server hosting the share, instead of the actual server name. When creating the share for the file share witness, use the fully qualified domain name (FQDN) for the CNAME record instead of the server name because this practice assists with site resilience.”

Upon review of this guidance, we have learned that its effects and success can be unpredictable in some environments. As a result, we decided to revisit this guidance, and after working closely with the Windows Cluster team on various site resilience scenarios, we have decided to revise our configuration guidance.

In summary, we no longer recommend using a CNAME record as part of the FSW provisioning process. Instead of using a CNAME record and changing the FQDN for the target host to point to a server with a replacement FSW, in a backup site activation process, or in the reactivation process for a primary site, we now recommend using the Cluster service’s built in “force quorum” capabilities.

Read more at source: http://msexchangeteam.com/archive/2008/04/03/448615.aspx