Hi,
It sounds like you might have too much pressure on the presser foot. For normal piecing a good deal of pressure is ok, but for quilting, even stitch-in-the-ditch, if the machine is pressing down on the presser foot too much, it can cause puckering at the "crossover" lines.
I made a video about it and put it up here: Sewing Machine Pressure Settings:
http://www.youtube.com/watch?v=Ox8qRhWF3CI
I hope this helps :)
Marguerita