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.