Good point, you've got extra circuitry there that could be injecting noise into the analog section. The midi interface ground wire connection should have been made back at the power supply.
One telltale sign if the interface is at fault, is if it's a midi input and you exercise it via an external controller (slider etc.) you will hear a related 'zipper/buzz' effect as you exercise the control and send related midi controller data into the Polysix.