On startup, the agent checks for status file for the previous PID, and if it is taken then it will give this error:
CA-System Agent R11-3-AGENT Already running (pid 9539)
Normally, when the agent is shutdown properly, the status file will not have any PID in it. It will just have 'Inactive' in it.
The agent should always be properly shutdown. Use the Services console or the 'cybagent-R11-3-AGENT.init' script to start or stop the agent.
If the agent does not start, and gives the 'Already running' error then: