It appears as though the Pat light (Signal Tower) is tied into the Cycle Start of the CNC. That way, when Cycle start has been activated, the green light is on. Unfortunately, any cycle start will activate the green light, whether in Auto mode or MDI mode.
You can try tying in the green light of the signal tower to the Spindle On signal, that way the light will be on only during spindle operation. Or the other option, which may be quite expensive, is to get some type of monitoring software, like Predator, or something.