Honestly, I think you're chasing symptoms without a diagnosis. The flippers are on a totally separate circuit from the 5v, so there are a lot of places the problem could be hiding.
I'd get in there first and start testing, look for where your voltages are insufficient and dragging down the rest of the circuits. Check the +5v circuit both on the power supply and the CPU board test points. Test the flipper voltage too. Heck, also check the voltage at your wall socket, and again at the power switch in the cabinet (looking for a drop maybe at the varistor or line filter).
Any chance it may be a re-import, that was wired for a slightly lower voltage?