A couple comments, don't profess to be an expert, though.
1) boiler is angled, not flat. Perhaps all water in boiler is expelled on first puff, none left to cool, and suck water back in.
2) Is burner inserted backwards in photo? At any rate, flame may be licking the tubes. If they get, and stay, flame hot, then perhaps no suction available to refill them. Easy to check, just put a barrier between burner flame and the tubes.
Neat hull; I make bottleboat sailboats, but hadn't considered a bottleboat popper :-)
Mogogear is an expert, you might mail him, though I expect he'll see your thread eventually.