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I have run jstest on both controllers and no issues apparent with them i.e. when pressing the B button i get on/off with no other button or dpad direction showing as being pressed at the same time.
You mention emulator configuration I do not recall configuring the emulators specifically, I have only run the wizard in ES and Register RetroArch Controller under retropie_setup.sh for JS0 then replicated that in retroarch.cfg located at /opt/retropie/configs/all for JS1.
where would these emulator configs be so I can check?