Ok, a few more ideas:
– You need to delete the file /home/pi/.emulationstation/es_input.cfg to have Emulation Station show the input configuration screen again.
– Also, do you put the crimp connector onto the pin headers with the right orientation? GND should be on the outer two pins as shown in the diagram attached to this post.
– There is a program for explicitly testing the button located in /home/pi/RetroPie/supplementary/SNESDev/supplementary/testButton/. If this directory does not exist,you need to install SNESDev together with the BCM library via the source-based installation of the RetroPie Setup Script. If you select only SNESDev and the BCM library this will take only a few minutes.
– Orientation of the adapter itself: The pin header has to point to the inside of the RPi.
Maybe one of these points give you a hint?!