The rollovers should all fire the E/"3000 Point and Advance Sequence" relay. If some aren't have a close look at the Sequence Unit which is probably a step unit with 2 coils (advance and reset). There may be a problem with the first two contacts on that unit.
Atlantis E relay (resized).jpg
With the game unplugged check each position of the step unit to see if you can measure an ohm or less resistance between the blue-white-red wire coming out of the Sequence unit and one of the wires coming in from the rollover switches. So in the 2nd position for example you should see an ohm or less between the blue-white-red wire and the orange-black wire. In the 3rd position you should see an ohm or less between blue-white-red and brown-black. If you get a higher resistance in the first two positions that could explain what you're seeing.

/Mark