When i work on flannel I have found that it shrinks..wash before and dry hot! I don't wash hot. I don't use softener. Try finding the way your flannel works.. does it stretch? Most don't. Tape the bottom to your work place to make sure it does not shift to "sandwich." I am assuming you are not using batting...do pin (flat head pins) about every 4 inches. Machine speed slow. Only thing i can think of.
I made changing pads or lovey cloths with satin of sort and flannel "quilting" every two inches. These squares were about 14 inch square.
Other than that use flannel for quilt backing and have to unpin and smooth ad I go.
Love to know your outcome..good luck!