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.
Evidently when the SCOM Management Agent is installed an SSL certificate is generated by the agent to allow for encrypted communication back to the SCOM server. Since the we changed the hostname after the agent was installed the common name attribute in the certificate was incorrect.
We resolved this issue by deleting the certificates created in:
/etc/opt/microsoft/scx/ssl/
and then ran the following command to regenerate the certificates:
/opt/microsoft/scx/bin/tools/scxsslconfig
Restart the SCOM agent services:
service scx-cimd restart
The SCOM agent should be good to go for discovery now.
Enjoy,
Flux.