What kind of noise? Does it sound like it's coming from the motor, like a hum or a grind? Or from the bobbin area, like a thump or click?
Did you change the needle? A bent needle could be hitting against the foot. Are you sure the pressure foot is attached firmly? Does it make the noise when sewing through thinner fabric? Are you sure the bobbin is seated properly? Since flannel is pretty linty, there may be a gob of lint under the plate that covers the feed dogs. Did you take that off and brush it out? Lots of other things to check out, that I can't think of. Maybe someone else can add to the checklist. If everything else has been eliminated, then you may need to take it in to a professional.