That's not a Boat. It's an AI Boat. AI Boats aren't properly registered with the ship-entering logic. Crafting it back into a non-AI Boat makes the controls work fine.
AI boats also break the pathfinder, so they drive in straight lines without avoid collisions with entities (like signal buoys) or terrain. I should probably do something to disallow the creation of AI boats altogether, as I don't consider them to be useful.