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I performed a firmware upgrade on the J-Pac (causing annoying control mapping problems that I won’t get into here). Then I zapped the sd-card with a fresh copy of RetroPie. Now I can edit those files and get the expected results.

Since I haven’t had the same problem.

With the last install, I played with several joypads, a bluetooth wireless NES controller, and fumbled with all the configuration tools.

I’m not sure how it got hosed or why, but the fresh install got me going!