One cause of this is when you have some areas closely quilted and others not quilted at all. If you think about it, quilting stitches require the fabric to "bend" frequently and this causes the scrunching. This may be only part of your problem, however.
How did you baste the quilt? I'm thinking that, for quilting of this type, you really want to spray baste. Spray basting keeps all three layers in continuous contact with each other, providing some resistance to the "take up" of fabric that causes scrunching.