I've had that trouble with a spray basted large quilt, due to shifting of the top (even though it was well adhered) when moving it through the machine. So what I now do is spray baste both the backing and the top, get them on and then add some safety pins here and there maybe 10" or so apart just to hold it together until I've finished stitching in the ditch. I ditch the whole quilt before I take out any of the pins. Doing those things has eliminated the problem for me, but I FMQ, I seldom use a walking foot. If this is only happening when you use a walking foot then I would add some pins to the spray basted sandwich and plan on ditching everything to get it stabilized before removing the pins. I would also check to see if you need to loosen the pressure on your pressure foot if your machine allows for that.
Rob