As it turns out, the board with the safe shutdown circuitry was missing a resistor near the fan header, so the path that needed to be made to induce the script was not being completed. Retroflag was kind enough to send a replacement board, and now it works perfectly. No script modifications required. See the included picture for details.alt text

@hoodle The wires inside the nespi case are pretty thin. I do get the low power warning with mine sometimes, but mostly fixed that by using a 3A supply. Still get it once in a while when loading movies in KODI. The only way to fix it is to rewire the case with thicker cables.

@haemogoblin Yes, it works exactly like that by default for libretro emulators Select and Start exits to the menu. To begin, you should read this https://retropie.org.uk/forum/topic/3/read-this-first and provide info on your setup quickly followed by https://github.com/retropie/retropie-setup/wiki/First-Installation#configure-controllers which explains everything you are asking.

Not the exact diagram I used originally, but this one will still show you the pins to disable or remove

https://www.psdevwiki.com/ps3/File:Usb-pinout.png

You need to disable/remove the +5v/VCC power. This will then turn that USB cable into a data only cable. As your hub is a powered USB hub this won't matter. Thats why when the PI is off its still powered as the hub is now feeding +5v back into the PI. Not a great idea as its not really designed to be powered from a USB connector plus the problems this could cause with too much current draw through the USB connector that the PI needs

Either by removing the pin that supplies +5v in the USB plug to the PI or carefully peel back the cable insulation and snip the red wire for the +5v

@elvycoll Consider to buy a NESPi+ case
Maybe you can buy a Pimoroni SHIM instead...