Short version - It is probably you. I had the same problem, but think I have it solved (I'll know in a week!).

 Long version:  Mine are doing the same, and when I did do the final dry stitch one of the deck panels (the last 12" of the bow) actually popped out as I couldn't get it all to line up while the rest of the deck and base had just been tacked with epoxy.   I ended up scraping the epoxy off this part (one side of the bow) and letting the epoxy set for the rest of the boat while the deck was tied down, and then after it was set I pulled the deck off and reset the 12" portion that had popped out.  When I let the deck just sit there, there is a noticable wave, maybe 1" worth of in/out over about a 18"of the front bow. The back seemed fine.

 You can see the warble here, but maybe compare against yours: http://www.flickr.com/photos/cowans/5347729193/

and here: http://www.flickr.com/photos/cowans/5348350388/#/photos/cowans/5347732763/lightbox/

And the after assembly popup here: http://www.flickr.com/photos/cowans/5348341230/

*** HOWEVER, I think it will work out b/c when I let the epoxy set on the popped out piece and then wrapped it back on to the base (with saran, not wires this time) to set with the edges of the deck and the base lined up, the wave disappeared.  I think the key was to get the chamfered edges of the base and the deck to line up perfect, and the forces of the 2 parts seemed to bring it all into alignment.  It wasn't easy, and took 2 of us about 45 min to get just the bow lined up for the 12" "reset" piece. 

Through trial and error, here is what I would do again that works:

1) I also seemed to put 2x the amount of stictches in some of the sections to keep it tight. The stern and bow, specifically on the deck.  When the deck/bottom are tied together, it pulls both back to shape. 

2)CLC should consider adding another temp bulkhead at the bow, specifically to push up the bow when you are stitching it together. Like I said, mine collaposed and I couldn't get it set without pulling the whole deck off. With my epoxy setting, this wasn't an option so I had to leave it and do it as a 2nd try.  Maybe it's more a building trick that needs added in.

My next step is to do the inside fillet and glass, then put it together again so that will be the test if it all works.

btw, if it makes a difference, i didn't order a kit but cut them myself so I assumed some of the error is in both my cuts + my chamfer + the scarf is at the bow where the waves are.

 As a first time builder, even though i'm pretty experienced with other finishing work, the manual isn't very good and seems to skip some of these important notes and tips.  I got alot from looking at other builds on the 'net and seeing their pictures to make sure I was on track.

If you need it I'll try to post a pic this week of the final "resetting" as it is tied down (the boat is at a shop I need to drive to work on, so can't get one now).

Good luck! Don't forget to post your end result - i've learned alot from the forums when people do that.

Actually, mine looks very similar to yours. Mine is much like your second picture. Since I am farther along, my mistake has now been filleted, glassed and cured in place! I thought I had it sort of acceptable but the front part popped up to a flatter angle sometime during the night after I put the fillets and fiberglass tape on.

  I'm pretty disheartened with the results. The hull looks nice but the deck is just unacceptable. At this point I should be attaching the deck to the hull, but i just can't do it. I don't want to mess up the hull and end up with a boat that looks bad. I did a nice job on my Night Heron Hybrid a couple years ago, so I know I can do this thing right.

 I would just buy a new deck and start over, but I have no confidence that it would turn out better the second time. So I'm kinda stuck here. I'll be looking forward to seeing how yours and the next few turn out when it comes to attaching the deck to the hull. If you and others can get the deck to look right, I'll have more confidence about buying another and trying again.

If your last step after glassing didn't include to re-attach the hull / deck together to ensure it forms in the correct place, it may still work without a noticable bump in the deck.  I am fighting more error than you as I didn't do the best job on cutting to the lines exactly onto a sheet (learned my tips on cutting nicely 1/2 way through the cuts)

Even if not, I would think if your inside of the hull is glassed, and the deck is just filleted and glassed on the seams I think you'll be ok as although the seams are now set, the ripple on the edges of the sheer panel may still line up. You shouldn't have glassed the outside of the hull & deck at this point, they get glassed when the whole thing is together (at least according to the manual, even though the pictures don't seem to show that - either that or the shearwater they show you can't see the deck attached).

Try to dry fit the hull / deck together with some straps &  shrink wrap, and see what it does.

I'm going to the shop tonight to prep the hull & deck for the epoxy, so I'll see if my ripple has disappeared....

Ok everybody, I called Joey from CLC about this. He got together with a few people including the designer Eric Schade. They told me to just wire the wavy looking deck down to the hull and everything should work out fine. Evidently it's SUPPOSED to look that way at this stage.

  SO... over the past couple days I did as they said...and IT WORKED! My deck is now attached, tacked, filleted and fiberglass taped to the hull and the waves are completely gone. (Since in my case, I allowed the angle between the Bow Sheer panels and the bow deck panels to become too flat, I had to use a cutting wheel on the Dremmel to separate the two and re-do the joint with a greater angle)

  Lessons learned:  

1) Make sure the angle between the deck and sheer panels are about 60 degrees.

2) Don't worry if the Sheer panels develop a bit of a wave.

3) Don't expect the deck to just sit nicely on the hull, it is going to take a little "encouragement" to fit properly, but it WILL fit properly.