Flannel is clingy and the poly batting may be slippery causing the flannel to go one way and the batting another. The flannel is also thicker than regular cotton so you might need to lighten the presser foot pressure which can't be done on some machines. I can do it on 2 of mine but the 3rd one, it is what it is. If you can't decrease the pressure, definitely try starching the snot out of the flannel or putting on the darning foot and dropping/covering the feed dogs and do a wavy line instead of stitch in the ditch or go full blown free motion.
Another issue with flannel is the tremendous amount of fuzz it leaves behind. That may have built up in your feed dogs and walking foot causing them not to work as well or at all. You'll have to clean them often with flannel. Starching will help control the fuzz but it won't eliminate it.