We first hear this sound in reference to the "Navy hydroplane" that Walter steers through a violent storm; he imagines it's the "pounding of the cylinders" (1). Later, in Walter's fantasy surgery, the "new anesthetizer" gives way and makes the same sound (6). Finally, when Mitty imagines himself a British pilot, flame-throwers make the same noise. It might be that this is the sound of the car engine, which Walter first hears when he's driving into town with his wife – although we do hear the "pocketa pocketa" again when Walter is sitting in the lobby, not in his car.
Regardless of where the "pocketa pocketa" originates, we do know that the sound provides a solid link between the real world and Walter's fantasies, as well as a common link between his multiple fantasies. It's one of the many comic elements of the story – the same funny sound cropping up over and over again – and it lends a tangible, permanent element to Mitty's various fantasies.