Sasha -
Unfortunately, factory seconds are just that, and may come with one or more defects, ranging from cosmetic to who-knows-what.
If you are good with your hands I would recommend giving it a shot yourself for anything short of plastic welding. Even then, I've had kayaks back to the dealer AND to the factory and they still didn't do a weld much better than I.
Beware of anyone who says they will fix cracks, etc. with "hot glue" or "goop". It's your butt out there two miles in the ocean.
I'm willing to bet that your current problem is from too tight a hatch installation and that you can take a sixteenth off the hatch just a well as anyone, better than most.
My $.02. Unfortunately (or fortunately) it's all part of the learning process for almost any yaker...
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"I Brake for Halibut"
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