I have been unable to have the get the Sonic emitter - Robo-scorpion to be recognized by the Juke Box. I tried before completing the final mission, after and a couple of time when returning.
Did you do anything special?
Did you complete the quest Field Research? If yes, then just exchange one emitter for the Robo-Scorpion. If you do not have the option then you have to find the audio file for it. Complete Field Research Quest. It is the the Forbidden Dome when you destroy Mobius' robo-scorpion, on a table at the far end of the room.