One of my points here is that Hobie needs to make a more robust seal for the front hatch.
I more suspect a misfit cut of both hatch cover and hatch opening in hull.
I did not have a leak problem until my hatch-opening seal came loose. I re-glued it. My re-glued hatch-opening seal looks good, but my front hatch began to leak seriously on our recent camping trips. If you think about it, when your front hatch leaks, it is both seals that must be leaking.
What you are saying is in fact that your hatch-cover seal
was leaking from the beginning, and still is. Also that your hatch-opening seal
was the only watertight seal from the beginning. But when you re-glued the seal, it did not came in same position as the one Hobie factory mounted. If you pressed the seal down properly until it stopped (as I think you should do), maybe it followed the wrongly, to deep cut (longsides) in the hull. I claim that Hobie did not glued the seal in line with the cut in the hull. But you did. Therefore it now leaks. (Sorry for my bad english but I hope you got what I meant)
Oh yes, this is just a theory! But I have my own problems with front hatch leaking and my thinking is somewhat orientated around what I see on my own hatch cover and hatch opening.