I put a heavy bead of silicone all around the inside of the foam gasket, as well as around the screw holes and on the "washer" side of the screw. I've had no such problems to date, of which I'm aware.
There are a couple of holes not used for attachment, so I suppose water could make its way into the spoiler, though I have to wonder how deep the water got.
The only (possible) solution I can think of is to remove the screws, then remove the spoiler (use fishing line to cut the silicone between the spoiler and the trunk as needed), clean up the old silicone, then put it back with silicone all around the inside of the foam gasket.
Good luck.