Here's a pic of what I described!

pretty hard to tell from your pics what is going on. Also, not sure what you're talking about regarding the "invisible hold down system". I am assuming that may be the bungee hatch restraint system. All that I can say is that I have a chesapeake 18 with flush hatches and using the bungee hatch restraint kit that CLC sells. Kit supplied gasket material. Takes maybe 1/2 hour for the hatches to go totally flush. Maybe longer for the first time but I didn't bother timing it. But I'm really more worried about getting a good seal rather than a perfect flush fit. My hatches are seaworthy and that is what I look for. 

Ok, here are the clc links that pertain to my situation:

http://www.clcboats.com/shop/products/boat-gear/kayak-gear-accessories/bungie-hatch-hold-down.html

http://www.clcboats.com/shoptips/fitting_out/flush_hatches.html

Maybe a few more days will help the seal compress a bit more!

Chris F

You need to have a spacer between the underside of the deck and the top of the sill piece that equals the width of the compressed foam.  

For now you can paddle all you want and it should stay dry.  If not tty to tighten the bungie cords a bit.  

You can probably cut the sill back to match the hole and then glue a new sill under that.  In one place, I put in a day hatch and ended up cutting the foam a bit thinner since the spacer I used there was not quite as thick.

Ed

I may just have cut my sill out and make a new one leaving a space just like you've suggested...thanks!

For now I've removed the CLC foam, and I've replaced it with some 3/8 inch closed-cell insulation from Lowes that initially seems to be compressing better than the 1/2 inch wide CLC foam.

Thanks for your help,

Chris F

Chris,

I followed those same directions. I have hatches from 2 laminated pieces of 4 mm ply and there are (2) 4 mm sill spacers between the deck and the hatch sill. That worked out well for me, but it does take some time for the gasket to compress. If it hasn't compressed in a day or so, Ed's suggestion regarding cutting back the sill (now a sill spacer) and adding a new sill sounds like it may be the way to go. Try increasing the bungee tension first.  My hatches are usually flush (relatively speaking) in less than an hour.