What kind of pins are you using and how do you pin them.
Are you using the 1" safety pins.
Do you pin but not close them until you have an area pinned?
If you close when you insert the pins there is a tendency to pinch the fabric and the back won't lay flat.
Wait until you have an area done then close. Use one of the "Kwick Klips" or spoons to help close them.
Also, as I an free motion quilting I will often put a few long straight pins just in front of the walking foot to help keep the layers flat.