I had this same issue on two different WhirlWinds that I worked on. Both times it turned out to be faults with the switches where one had a bad solder connection which I reflowed solder to and the other had a bad switch that would randomly register (I just replaced this switch). Don't just check the top of the switches, but look at them from the underside of the playfield, making sure there's no loose wires or other obvious issues to the connection.