I am also currently working on a Ship Ahoy and had a similar startup problem and discovered a couple disconnected wires on my AX relay. After reconnecting them and cleaning/inspecting all relay switches, the AX still needed some adjustment. These short throw, make/break relays can often be a bit fussy.
Still a few things I need to fine tune on mine yet. Mine awards Wows for hitting the right rollover sequences but not on score. My score pins are in the correct slots in the backbox. Anyone know if this is tied to a relay adjustment? I have the schematic but haven't looked yet, I've never been that proficient with them. I'm sure I will find it with a little studying but if I can fast track it...
Maybe it's the score reels. Still haven't gone through them. I hate working on Decagons.