How taut is your sandwich? It sounds to me like your backing may be a little lose (or is that loose?).
I tape my backing dow with blue tape and keep it very taut (but not overstretched). Then I lay the batting on in halves and pat it out until it lays very flat. I repeat with the top and pat it down - slightly smoothing it out from the center out. Then I pin about hand-width apart. Since this method, I have not had any puckers.
Have you tried on a trial piece to see if the problem with the walking foot?