If you start the Agent via the System Overview --> Agent... (that mean the agent is configured to the Services Manager in the Agent Properties).
So when you start on the overview page but it state that it is already running, it is referring to the process on the services manager already running.
The fact that on the Services Manager side that it is running/green.... but is still gray out on the System Overview just indicate that the process for the agent is active but there may be issues/error that not allowing the Agent to be "active" yet within the AE System/System Overview.
I would check that window agent TEMP folder and look at the latest logs and see if it stuck/looping on any error... (which it just cycling and repeating but doesn't cause the process to end/stop...).