Safe Shutdown Switch Help (Camble V1.2 & Other Issues)

[BazzJay]

I haven't worked on my GBZ for ages and decided to finally finish it.
I'm at a stage where I stopped because I couldn't figure out to get the safe shutdown from Camble to work and only recently I got it to work (Somewhat). (Using Camble's safe shutdown board v1.2 & script)

Is the safe shutdown meant to work inside emulation station?
I only figured out that the safe shutdown does work after some config editing and quitting emulation station before flicking the switch. I've checked the logs and it runs as it should. But if I do it while emulation station is running the system loses power instantly.
I would have assumed it quits emulation station and then it shuts down. Is this normal or if not is there a way so it works?
Edit: Now it doesn't work at all and I've done nothing. I've checked logs and it says it's running yet it doesn't work!

Other Issue:
This came up only as I started to work on the GBZ again, just randomly as I was shutting down using sudo halt or shutdown -h now.
Rebooting normally through emulation station and out of it works, but shutting down normally either in or out of emulation station gives me the kernel error;
Kernel panic - not syncing: attempted to kill init! exitcode=0x00000000 (With more of the error afterwards)

I have updated everything and i'm running RetroPie 4.4 on Raspi Zero W.

I've looked around for ages but can't find an answer to both these problems.