Server Automation == TrueSight Server Automation?
If yes, and there is not a server entry in the RCP console, then that means that the server has not been added into the TSSA inventory. This could be because there is no RSCD agent on the server, or more simply that the server has not been added into the TSSA inventory.
If the server exists in the TSSA RCP console, but is reporting the "agent is not communicating" that could be either the RSCD agent is not running or a communications issue preventing the TSSA application server(s) from talking to the agent. There are several avenues to troubleshoot this particular problem, but that may be a bit outside the scope of the question you asked.
Thanks Greg for the reply but this was about a server not being automatically mapped inside the vulnerability manager console. Anyway, I've already got my answer from support on this and just wanted to follow up that this is resolved.