I had same faults occuring on a swift 5000 with a magnetec dsd 412 drive. I did everything you've tried if not more trying to fix it. The conduit for the velocity Encoder wiring was grounded and the shield was grounded on one side like it should be. I started out by pulling the wiring out of the conduit, temporarily running it out of the bottom of the drive across the floor to the encoder so I knew it was far away from any other circuits that could create noise in the line. The problem went away and I'm fairly sure the noise was from the way the wiring was ran from the bottom of the drive to the top of the controller.