I have had the same problem and taken my machine and BSR in twice-supposedly there is nothing wrong and they have updated everything. However, I notice that my skipping and stopping happens on dark fabrics, especially solid black. I just don't think that the BSR reads the darker fabrics well. In some cases I can't use my Bernina/BSR at all to free motion quilt. I made 4 black and white quilts this spring/summer and it happened on each one everytime I hit the back fabric. In between I have quilted several other projects with lighter fabric and no problem.
If I have marked a pattern with chalk heavily, I do give my BSR head a quick swipe to clean off eye.