I purhcased a UCC for Exchange and Lync, but the problem is they are two difference domain names. For example: Lync uses the domain example.net, Exchange uses the domain example.com, and our internal domain is example.local. So I placed all the names on the cert that are needed to make Lync and Exchange function. I placed FQDN for .local .net and .com on the cert. The primary CN is termana.net on the cert. When I install the cert on my Exchange server, users are unable to authenticate with Exchange. It just keep prompting for username and password. Does the primary CN have to be mail.example.com in order for Exchange to work properly?
Did you have a look here
The answer might be there in the FAQ