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I am using .cue/.iso roms in mednafen-pce.
Make sure you have the syscard3.pce in your BIOS folder. Then check your es_systems.cfg (probably in /etc/emulationstation) to see if your entry for the pc engine has .iso added to the supported file endings. Also if you are using .cue files check if the filename of the .iso file is the same name as the one written down in your cuefile. (it’s case sensitive)