Firstly this little board it great!
Just a heads up! FYI for those installing with MainSailOS on a 3d printer... although I'm not 100% sure this is the cause of the GPIO issue, doing this certainly cured my installation.
After wiring up and installing the ATXRaspi script as per instructions, the script ran on each reboot, however the ATXRaspi did not react and had no green led.
As I understand the green led means the ATXRaspi does not receive any RPI signals.
I had spent several hours trying to diagnose the problem and the solution was to alter the default GPIO pins in "shutdownirq.py" from 7 & 8 to 20 & 21.
After reconfiguring the GPIO pins, upon rebooting instantly the ATXRaspi reacted with a green led and the momentary button worked as intended.
Super, thanks for sharing and detailing the procedure!