I don't think the 3 season or the toolbox was meant to be watertight, more water, cold, and mosquito resistant. Sounds like there is some wind involve to blow the water into the toolbox. If you can't make the toolbox watertight, you may consider treating it as such and don't keep anything in it that is sensitive to moisture. I use it like I do my deck storage box at home and store items like my gas grill cover, etc. I drilled a hole in it and use a marine plug as a stopper to keep water out while traveling, but as a drain if it gets in when it rains or when I hose out the garage.
Personally, I would have preferred the roll down screen, but the 3 season doors were already on my rig when i bought it. It almost came off when I 1st purchased it, because it reduces my 12' garage down to 11' and my Mule is 10' 10".