I had this problem with my Janome and it was most frustrating. What it turned out to be was the fabric/needle combination. I was sewing with batiks and there was one blue batik where this was happening. I changed my needle to a sharp so that it was piercing the fabric better - prior was using a universal which had a duller point - and that took care of the problem. Because of that I rarely use universal needles anymore and just stick with a topstitch or sharp which both have a sharper point. Top stitch has a larger eye on it.
I also occasionally have skipped stitches when I am sewing over bulky seams too. Look to see if there is any pattern to where the skipped stitches are. A particular fabric, seam etc. That might help narrow down the problem