Maybe the shorter stitch would help too - may try that next time.

I have made one flannel hand quilted quilt - queen size. I washed the fabrics and completely dried them in the dryer. I wanted them to shrink as much as possible, and they shrunk a lot. I used 1/4 inch seams. I made the quilt about 10 years ago and I use it every winter. I have to send it to a cleaners because it won't fit in my washing machine. I have not had any problems at all with the seams. Since I was going to hand quilt it, I used a jeans tread, I think something like size 20 because my LQS said regular thread would disappear in the nap of the fabric.