Wow, weird problem but it sure seems like something is shorting. You could really figure it out by cutting the return wire at the flipper temporarily and running a new wire to the flipper switch, let it droop down from the PF and over to the switch but long enough to let you open the machine. Something is grounding somewhere and this would bypass all that. If this works reliably, snip open all the harness ties and run a new replacement wire.