I am having the same issue, but unable to resolve using the various options to configure the controller.
Within any RetroArch powered emulator, my controllers can only move up and down now.
Tried using Emulation Station to set the controller buttons again, also used the options within the RetroPie menu for RetroArch joypad and Retro Arch Keyboard/Joypad.
I seen a log flash up when trying one of those methods which read “module ‘retroarchjoyconfig’ found for platform rpi1” – which sounds good, however there was no interface to define buttons at that time.
This is such a bummer, makes some games completely unplayable. Sorry to hear you have the same issue, please let me know if you resolve it! Apparently there is a debug code you can run, which I intend to do when I get some time.