[Dakota773]

I found that my 98 31 open had some leaks in heavy rain from the front hatch, but not from the hatch seals. 

The 5200 setting the hatch had degenerate enough to let a small amount of water in in heavy rain. In the off season, i carefully tapped off the deck and used a putty knife to "clean" or at least drag around the lip as deep as i could.  Using a flat blade i lifted the hatch deck lip and drew a bead of caulk (4200) under and around.  Releasing the blades and the overall pressure drew the caulk tighter and with a little clean up it was done no more leaks. Not as good a totally removing the hatch and resetting it, but it did the trick.

If it's not the rubber hatch seal, you might have the same problems.