For those asking here is what I did:
I did a: sudo apt-get update and: sudo apt-get upgrade
I did a firmware upgrade: sudo rpi-update
I turned on the setting in sudo raspi-config
I also did a git pull on the ControlBlockService2 repo and there were a bunch of updates there since when I grabbed it a week ago. So I then had to do a: make clean, then do all the steps to compile and install it again.
After that I was able to set the config file with the correct type of ’snes’.
I restarted and then before even trying the onscreen setup I logged in via SSH and ran jstest /dev/input/js0 (or js1) and checked to see if the buttons were being detected, and luckily for me they were!
Hope that helps.