So I bought a PetRockBlock GPIO adapter and soldered it myself. I’ve tested it’s working using the button press test and both my SNES joypads are fulling working according to JSTEST on JS0 and JS1.
The problem I’m having is that if I test JS3 every now and then it detects activity across all buttons at the same time. It’s the very briefest of flickers but this means I can’t configure Emulations Station properly because when I’m trying to configure a controller, this flicker of activity happens and ruins the setup.
It sounds as if some other service is emulating another joystick device. You can get an overview about the services with the command sudo service --status-all. The RetroPie GPIO Adapter needs only SNESDev to be running as service.