i use flannel all the time...i think you will have better results if you lengthen your stitch a little bit it sounds as if you are using too small of a stitch for your sandwich, remember flannel is a (thicker/heavier) fabric, then add the top and the batting...makes a thick fluffy sandwich...a longer stitch and on my machine i can set it for light, medium or heavy fabrics which adjust's the pressure on the foot to accomedate the thickness. when i've had pucker problems though it's been fixed with a longer stitch.