Another possible source is the door itself. Luckily I haven't had water getting inside the area under the bottom bunk yet, but when I open the outside compartment door and prop it up, water leaks out of the door itself. Apparently water is running down the door and getting inside the door between the outer door panel and the extruded aluminum material that goes around the perimeter of the door itself. When I have the time I will disassemble the door itself and check to see if there is any water damaged material inside that needs replacing. Then I will put the door back together and seal all the edges inside and out with Proflex as I put it back together again.
Mine is the rectangular door with the square corners.