Watson,
If you are using a floating rather than a hopping foot, try lowering it even more than you already have, so it is almost touching the top of your quilt (just a hair's breadth away). I had one quilt where I needed to do that when I was using my Westalee ruler foot. It made dealing with seams a pain in the butt, since I had to re-adjust the height of the foot at every seam. That was when I decided to spend the money for the Janome convertible FMQ set and the optional ruler foot that attaches to it., There's a thumb screw on the Janome convertible FMQ that allows you to easily adjust the height of the foot while quilting.
I never did figure out why I needed to adjust the foot that much for that one quilt.
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