@juanzt that cool. I have also found that just changing .bin to .iso works on psx emulators. Doesn’t seem to effect anything unless a game uses CDDA. It just won’t play the cdda.
Runcommand is meant to be run interactively - if you want to run it, make sure it has a controlling terminal attached. If you wish to just start the emulator & games, then why are you using Runcommand instead of starting the emulator directly ?
[WARN] Input device ID 3 is unknown to this libretro implementation. Using RETRO _DEVICE_JOYPAD.
That's because of the RA's configuration - try resetting the configuration to default by copying the retroarch.cfg.rp-dist files over the retroarch.cfg in the /opt/retropie/configs/all/ folder.