Spindle starts upon exit of Linuxcnc. How to stop?

The fault output should follow the state of the G540 fault LEDa
Are you saying the fault signal (GPIO03 in hal) is high but
you have a green light?

So I guess I must have messed up pin 3 on the 5i25 board some how. I mapped pin 15 to 17 on my lpt cable and everything seems to be working properly.

Thank you for the help.