I use a walking foot when I SID and I recently learned that I need to slightly spread the seam with my hands to be able to get IN the ditch. As soon as I release my hands, the stitch disappears.
If the seam switches sides from block to block (the seam allowance is ironed to the opposite side) I was taught to slightly ease the quilt so the needle can gently move to the opposite ditch. This makes the seam allowance transitions seamless. It really works - I was amazed, because I always used to have these ragged chunky transitions.