Lamonte,
Normally, a rain water leak into that compartment is caused by a leak in the compartment exterior walls and not the door seal. You can check for a leak in two different manners. First, put a bright lantern (preferable battery powered) into the compartment with the door closed on a dark night and look for any light from a hole or crack in the compartment.
The other method is to use a blow gun and direct compressed air from the compartment interior at all seams or possible leak locations while someone looks and feels of the exterior for air flow. Sometimes a soap and water solution is helpful when looking for the leak with this method, but it is usually not necessary.
Gerald