Is it the vibration of the flippers causing the G.I to flicker?

Either way, I'd remove the driver board and with a DMM check the G.I traces from the plug to upstream components.  I would also check the underside of the header pins for cold joints.

Secondly I would check the G.I plug which goes into the transformer (yellow/white & yellow) and reseat the connector a couple of times. (with power off and unplugged of course).

Is it ALL G.I doing the same thing or certain strings?