Rachel, You are NOT a pain in the butt! Your hubby paid good money for that machine and all the options like the BSR and you have a right to EXPECT it to function correctly! I feel so bad for you and your distress...you should be delighted with the machine, not in tears. If I may, I would like to suggest that you be politely firm with the dealer, explaining to them that you feel the problem must be the BSR because it FMQ's like a dream without it. It would be a simple matter to get a different BSR, plug it into your machine and see what happens. I know it is difficult, but I would take everything with you including he quilt you are working on and duplicate what you have been doing. If that BSR works fine then I would think that the problem is in the connection where you plug it into the machine, or with the component in your machine that deals with the BSR. In that case, I would politely request a new machine...sort of start from scratch.
If the BSR was so sensitive that it wouldn't sew over anything with seams then there would be no purpose to have it as quilts are pieced, therefore have seams and FMQ is a way to finish a quilt. I did extensive FMQ'ing on my hubbys quilt for Christmas, it had lots of seams and the only problem I had was my inexperience.
Once again, insist that the dealer make this right, don't feel bad about bothering them...you are the consumer, and if you didn't buy, they couldn't make a living. If they can't or won't make it right, then contact Bernina. I know a lady who got a new 830 (approx $11,000)before Christmas and had nothing but trouble with it...the dealer tried and couldn't resolve the issue. She finally contacted Bernina...and in a very short period of time had a new machine and never had another problem.
Good Luck! Sorry so long, but I feel so bad for you and don't want you to feel it is you that is the problem, because it isn't.