Spindle starts upon exit of Linuxcnc. How to stop?

Lobg time since i had G540's, but it had no fault output, e-stop was wired to an input on parallel port.
@x26iclone,
Please clarify what pins are you reffering to as both the G540 and parallel port have pins 10 and 12.
In this case it is the G540 pins.

Yes my estop is wired between 10 and 12 of the G540 terminal block.

Sorry for the confusion.

I believe pin 7 of the lpt port is free, so I should be able to jump 10 and 12 of the G540 terminal block together and then put my estop between pin 7 and ground of the lpt, right?

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.