I have noticed this weirdness when using a Alltek and other aftermarket MPU's. With an actual stern MPU-200 mine doesn't make the sound at power up.
Many solid state games of this era have the "hum" sound changing between HSTD and current score in attract mode. I think it's feedback from the high voltage displays coming through the ground circuit. Some of the higher amperage rectifiers used on the repro boards may be adding to this. I notice less noise when using low volt Pinscore or Xpin displays.