Well I guess the issue really is with the BSR because it went on to start skipping again this morning. In tears I brought out my old Brother machine and started FMQ'ing on it. Worked like a charm. My husband asked me if I had tried just plain FMQ'ing on the Bernina, just to see if it still did it without the BSR attached. I admitted I hadn't but figured I probably should. I went on to quilt for over an hour on my Bernina without the BSR and the machine never skipped once.
So I don't know if I have a faulty BSR (even though the updates were done to it yesterday) or if it's just so darn sensitive, you can't use it over anything but a plain piece of fabric (no seams). I feel like such a pain in the rear but I guess I'll take my BSR back in to the store next week and see what they say.