Do you get points on any pass throughs? If no check the first point relay and contacts. Make sure the relay is releasing and working properly.
Couple easy fist step would be to make sure contacts on the pass throughs and the contacts on the 500/1000 point relays are clean and functioning correctly. Might need a schematic. The pro's on here will be able to figure this out a lot quicker than me though. Just some of the first steps a rookie like me would look at.