I hope you have access to an oscilloscope because it is the only good way to track down this problem. The relay clicking is probably the spindle power relay. I'd start by looking at the enable signal coming from the computer and make sure it is strong and solid. The interference the controller boxes can kick back is a prime suspect because of the chattering you are seeing. I (think I) remember that the limits switches and/or estop signals were hardwired to shutdown the spindle in the mill so next I'd scope them for intermittent shorts. Either of those lines could cause that relay to actuate but not have the TTL level to fire a signal to controller for the software to see and shutdown the enable signal.