You mentioned it may have happened since the tuner was installed. The fact it happens on two unrelated empegs means it's more than likely an issue with the install.

Is it possible the tuner is creating stalk events? You say you had debug messages attached to the buttons. The stalk events are different to the button events (IIRC) although they may do the same thing like skip a track.

You could just temporarily unplug the tuner. If it happens just once without the tuner, you can at least rule it out then.