I double checked my settings tonight, and find I get better results setting Lower on the keyboard to Midi channel one, the default channel on the harmonizer. Put everything else on a different channel.
I tried using Chord One, Chord Two and Right One. They all work but the Lower and Right One work best by far.
I suspect the Harmony M just "sees" the notes being played either right or left of the split (or both) depending on how you set the controller or keyboard. It then determines the chords from those notes.
I also suspect that sending "chord" information might not be using the harmonizer best.
You might want to check this out.
DonM