Here's the thread I started that got a lot of response.
http://www.quiltingboard.com/t-35440-1.htm
In a nutshell here's what I came up with that really helped the skipping;
1) Get the hardware and software update done at your Bernina dealer. If they don't know what needs updating tell them to contact their Bernina rep and they should be able to tell them what needs done.
2) I have found a 90/14 needle works best for quilting with my BSR. I have used an 80/12 with a applique wall hanging, but the fabrics were batiks and the top had no seams. I didn't want very big holes so that's why I went with a tad smaller needle. But for regular quilt tops, 90/14.
3) Even though the manual says to lower the presser foot pressure to 0, I only lower it slightly from the standard 42. Somewhere in the low 30's to high 20's, just depends on the quilt top and how big the seams are. When you lower the pressure to 0 the fabric tends to "tent" up around the needle and cause the top thread not to catch the bobbin thread. At least that's my theory. :)
Those three things are what I think has helped my BSR to work pretty much perfectly. Good luck! I know it's frustrating when something doesn't work right, especially something as expensive as the BSR!