I had the same problem today, booking SAT-ORD flights. I am not on expert flyer (I just don't fly often enough right now to make it worth it), but when I put 2 passengers in the request, it went to the higher fare, but was able to puchase them individually, both at the lower price. This is a real pain as I was hoping to upgrade using my stickers, and the seperate PNRs make it a hassle (yes I know it can be done, but it's more work than just ticking the box).