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If you are using Version 3 Beta 2 I am starting to think there might be a problem with the autoconfig files.

My fix was as follows:
1 – Backup all files under config
2 – Delete them all
3 – Reconfigure each joypad using RetroPie Setup script and Joystick setup

Thanks! That solved it for me (finally :) ). Removed all the config files in opt/retropie/emulators/retroarch/configs and reconfigured my SNES USB controller again.