I've built wooden bulkhead doors more than once, but it isn't something I do for a living or anything.

Do you have wooden or steel bulkhead doors? Can you identify where the door is leaking, specifically? Steel bulkheads are designed with a lip, usually about 3/4" over which the door rests, to prevent any water running into the door opening. if this lip is compromised, that would be your problem, and you may be able to repair it yourself.