I don't know anything about the Berninas or the stitch regulator, but I do know that Universal tipped needles or worn/blunted needles can cause skipped stitches, especially in free-motion quilting. If you switch to a new sharp, it might eliminate the problem. Also make sure that your needle is seated correctly according to your manual.
I had the worst skipping possible when I spray basted - the needle kept gumming up and needing to be cleaned every few stitches and it was skipping more than it hit. The last time this happened, it was a vintage scrap quilt that I ended up throwing away. Nothing I tried could make the basting spray unsticky.
I don't know any way to fix the stitching that's already messed up other than getting out the seam-ripper and re-sewing those areas. Good luck!