I just did 2 twin size quilts with Snuggle Flannel on the backs. I had no problems at all on the quilting frame. It's very snuggly and both grandkids love their new quilts.
I always pre-wash flannel since a mis-adventure with it when I first started quilting and I'm more careful with my seam allowances now. I used 1/2 inch seam allowance for the backing and was very careful to keep it on grain. Some flannel can get stretched easily. I didn't have any trouble with the Snuggle brand but some I bought at Hancock Fabrics has to be starched heavily before I trust it.