I agree with your evaluation that the BSR seems to be doing the job as the needle is going up and down. So I guess that leaves the needle or the bobbin/bobbin hook. I wonder if fiddling with the bobbin tension would work?....hmmm...it seems to me that this is something the dealer should be able to reason out and solve. I would continue to work with them to correct this. I know what this machine costs and I believe that when one pays that much, that there is no reason to settle for "good enough if I fudge this or that". If they can't figure it out (and it seems that they are good people and will try) then email Bernina USA. I had an issue with embroidery software that the dealer couldn't resolve. I emailed Bernina USA and they were very responsive, communicated with my dealer and the problem resolved.
I have done FMQ without the BSR, but am not good at it so the BSR is my best friend. I FMQ'd a large part of a 70 X 74 quilt for my hubby for Christmas and even though it was my first attempt it turned out fairly well (my inexperience, not the machine kept it from being excellent).
Try not to get discouraged. I saw that quilt and it truly is a work of art! Love it! Good luck.