Ok, last ditch effort. When you launch a game, the box pops up onscreen. That is the launchcommand box. When you press a button you go into the launchcommand dialog where you can set video modes, etc. If you go into there, one of the options is "EDIT CUSTOM RETROARCH CONFIG FOR THIS ROM" - try typing the code manually into that area and saving. That will create the config file in your roms folder that you can edit further if needed.
If the file is created, and the effect still doesnt work, try putting nul in quotes ("nul") OR put a random number in there that the controller cannot support "99" would pull a button that doesnt exist.
If that doesn't work, im not sure what to tell ya, i use this method all the time for my arcade roms because they dont have consistent controls. I would use remapping but my arcade is all keyboard controls so retroarch config file edits work fine.