theruncommand script adds an addition config – and it seems retroarch breaks at more than 2 configs added to appendconfig – I have opened a ticket here – https://github.com/libretro/RetroArch/issues/1439
workarounds:
don’t use runcommand so the additional config is not added.
/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/neslibretro/fceumm_libretro.so --config /opt/retropie/configs/all/retroarch.cfg --appendconfig /opt/retropie/configs/nes/retroarch.cfg,/opt/retropie/configs/all/retroarchp2.cfg %ROM%"
alternatively, you can just add /opt/retropie/configs/nes/retroarch.cfg and “include” your addition config from there (putting #include path/to/additional/config in there)