I also have problems with flannel, not when piecing or even 1/2 square triangles but in the borders. The last two quilts I used I wanted the flannel in the outer boarders for the cozyness of flannel but it comes out wavy. I have tried cutting it across grain and down but they both come out wavy. I do measure the center and cut the borders not just sew it on. I don't know what I am doing wrong either but would love to know as I really like the feel of flannel. The last flannel I used was quilters flannel and not the cheap stuff.