One suggestion, have an overview tab that shows All. This way you can always check it in case you miss anything selected.
Also, make sure you are showing Agents in Space. I thought that was a separate item in the overview. You should see the agent’s ship and when you mouse over the ship there should be 2 icons, one for the ship and one for the agent.
What system is this? If I am not far I can try to check it tonight but that will not be for a while.