One thing I forgot to ask.... Did you pre-wash and dry the flannel? If not, it will shrink at a vastly different rate than the other fabrics in the top. At this point, if you haven't preshrunk the flannel, I would go ahead and do that before trying to add to the quilt top. (Wash and dry the backing as well.)
Actually, I wash and dry flannel twice before using it, as it can shrink even more the second time around. After that, it is stable.