Thanks to Robert's help, I got my GPIOs up and running, and good audio, with 3.14.26-ti-r43.
So, now I started to make my app launch at boot time. I created an init script for it, ran innserv, rebooted...and now my GPIOs are gone!
Unfortunately, insserv seems to do a lot to all the scripts, not just the one specified on the command line.
Do the init scripts dictate something about how the DTB gets applied? Could they have affected my GPIOs? How can I tell what DTB is in use?