Scheduler Usage

I often notice that after installing Control-M/Server and Agent that the local agent is listed twice in the Configuration Manager (and hence defined twice in the Control-M/Server), once with the short name and once with a fully qualified name. The one with the short name is the 'default' agent and cannot be removed. I can delete the instance with the fully qualified name, but it comes back after some time. I have no jobs attempting to run on that the agent using the fully qualified name and no utilities attempting to use the fully qualified name. Any ideas out there?