Could be that annoying bug that many people faced with the new version. Really what @Floob said; check the following file:
/opt/retropie/configs/psx/retroarch.cfg
If it has a lot of code you need to delete the file, update the RetroPie Install script, re-install the emulator(s). I had a similar problem with the Genesis emulators and this solved it, I hope it works for you like it did for me.