Rich
If you cannot make a lip or add a strip as Hermco has suggested, as another alternative you could try this stuff. I have used it to fill in the gaps. It is waterproof and flexs with the deck. You can get it at Home depot in 20' lengths for under $4.
Just stuff it in the gap after screwing the hatch down and then caulk over. I think Tom's idea of waxing first makes sense