I have my controllers set in retroarch, the other systems work OK with both sets (two identical usb encoders). However when I load up amiberry, I set both within the amiberry menu.
Works OK, but the config file seems to not have saved.
The only way around this is to set and save a config for every game, then save them out as an .uae, which is not ideal. Perhaps a Batocera related bug?