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!