What are you using for batting? And what is your stitch length?
My guess is that you are using high-loft polyester batting. This is more likely to pucker when machine quilting, especially if you are using your regular stitch length. You need to lengthen your stitch length for high-loft batting. However, if you are using polyester batting, you also have a different problem in that (in my opinion, anyway) you should be using cotton batting. Cotton will provide better protection for the hands, plus it won't melt when it gets hot the way polyester will.
If you are using cotton batting and your stitch length is correct for quilting (usually a little longer than for regular piecing or sewing), then I have different suggestions to make so you can machine quilt pucker-free.