controller fan not shutting down

My controller fan is not stopping after the time specified, 120 sec, The only way to stop the fan is to reset the firmware or restart the printer. I have a 2nd controller fan that I've set the overrides on and it continues to run after 120sec as well. It is triggered by the activation of the X stepper motor...although what is the X stepper on a corexy? Any suggestions on what to change/look for to get the fans to shut down after 120sec of no movement? Hmmm, what starts the timer for fan shutdown? Is it the stepper not moving for a set amount of time or is it something else?
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