Hmm, I'm not sure what could be going on. I've just confirmed that automation works on my machine using the latest 1.2 beta in Ableton Live 9. You are correct that this shouldn't require any MIDI connection.
Does moving a Function knob in Emote manually with the mouse affect the parameters as expected? Does automation move the Function knobs visually in Emote? Perhaps you could post some screenshots of the Emote parameters and the Ableton automation to see if there may be anything misconfigured.
