Are you sewing on different color fabric when you are having the problem? Are you doing your test swatch on the same fabric as your quilt? I had a similar problem and turned out to be the fabric. I was using 4 different batiks that were purchased at the same time from the same shop. I had no problems with three of them but the one blue I got skipped stitches. It was driving me crazy too. I cleaned the machine, changed needle, you name it I did it. I finally adjusted the tension until I got it stitching right and that did the trick. Different fabrics and even different color fabrics react differently.