Try running a line of stitches with the stitch regulator turned off. Then do the same with the stitch regulator turned on.
If both lines of stitching are skipping stitches, the problem is either timing, needle, the quilt is positioned too high off the bed of the machine or the quilt is too taut between the rollers.
If only the stitch regulated line is skipping stitches, clean your rails and make certain the encoder wheels are clean and adjusted to rest on the tracks properly.