I may have found it. I located a 4 wire harness underneath. I pulled it apart and reconnected several times and they are working correctly right now. The others were single wire connections (2 or 3 of them). If they don't retract on their own later maybe that's all it was. I'll clean the connection better tomorrow and then go from there.
rekoj71, thanks for the link. That makes troubleshooting much easier to understand.
ksh5000 "on newer models the door still controls the step position so it will extend if the door opens even if the engine is operating." That's the way mine should work. Battery is fully charged.