I don’t think it’s an issue with the roms at all, Have you registered the controller for retroarch?

if not go to the command screen (press F4 while in emulationstation) and do the following

1)Type “cd RretroPie-Setup” then hit enter

2)Type “sudo ./retropie_setup.sh

This will bring up a menu,
3)go down to “UPDATE retropie setup script” and hit enter, if you already did that before then skip this step

4)it should bring you back to the menu, if not just repeat steps 1-2, now go down to “SETUP” and hit enter

5)Now go down till you see something like “Register controller with RetroArch” (my wording may not be exact but it should be close enough) and hit enter

6) it will tell you to hit enter, do it, then it will tell you to hit enter again though on a black screen, make sure you have your controller ready, then hit enter and follow the prompts on screen, don’t worry if you don’t have enough buttons for all the comands, just let them “time out” and it will still save your config.

Now when all that is done, reboot your Pi and once in emulationstation press start and configure your controls, if everything is done right it should work now