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Hey, I had this same issue. The way I fixed it was to manually overwrite the retroarch.cfg file in the emulator config directory you are having issues with. Mine was PSX same as the OP.

All I did was make a new .cfg with retroarch in game then through WinScp deleted the contents of retroarch.cfg (located in /opt/configs/psx) leaving “input_remapping_directory = /opt/retropie/configs/psx/” at the top then copied the output from the saved file into the retroarch.cfg, save, restart EmulationStation and all is fixed… rinse and repeat until satisfied.

Hope this helps.