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Well, it looks like my problem was that I had followed this blog post: http://weekendengineer.wordpress.com/2014/09/02/auto-detecting-controllers-in-emulationstation-2-0
I had to deviate slightly from the instructions because the controller detection option in retroarch-config doesn’t seem to work (no output), so I ran joyconfig manually and copied the output to a file in /opt/retropie/emulators/RetroArch/configs. This apparently does not work properly.
I appended the contents of my custom config file to the main retroarch.cfg, and now the controller behaves properly (though it doesn’t switch mappings when I plug in a different controller, as was implied by that how-to.