We recently starting testing the SCOM 2012 Management Agent for Linux on a test server running CentOS 6.4 x86_64. Since we just installed a minimal set of packages via an automated kickstart the hostname of the machine wasn't set to the DNS resolved name.

After the SCOM agent was installed and even after we changed the hostname and setup the proper DNS the SCOM console was still barking about an SSL certificate common name matching the hostname of the server.