As per request on steam. My theory is that the issue is due to a reliance on the game to detect specific surfaces under ceilings to qualify as rain blocking. When such surfaces(floors if you will) are not in the permitted list, then it borks. Some combination thus either with water, the boat structure or structures placed on the boat structure/water are causing this or in reverse a check metric once a tile is placed above or similar.
FIRST_TIMER.zip