I just finished one that I made using EPP and when I first lay it down it wouldn't lay flat. So I carefully pressed and now it is as flat as a pancake. The other one I made, my first I used the tutorial on Missouri Quilt Co, absolutely the best tutorial on Dresden ever, and it too was a little wavy when I first lay it down, but then after several pressings it was nice and flat. Attention to detail is really important in doing a Dresden, no fudging 'cause it will show. Other than diligent pressing I'm at a loss at what the problem could be.
They are so beautiful so stick with it, you'll find the right way to get them the way you want and will love them.