Short version: I guess the BOS judges liked the other two beers better?
Longer version: Hard to say. Once you win your category, there's no telling how BOS will go. In this particular case, my beer was about 15 months old whereas it's peak is 9-12 months (Strong Scotch Ale). It was showing a little bit of oxidation (sherry-like) and that combined with the maillard products can produce raisin and plum-like flavors that can throw some people off, so although it was a very enjoyable scotch ale, it wouldn't necessarily do well against a couple of crisper and fresher beers. The 2nd place BOS also won a gold for that beer at NHC Final Round, so it's obviously nothing to sneeze at.
There were a couple other factors that may or may not have played a part. One of the BOS judges had a strong scotch ale so they may have been disappointed by the fact that their beer didn't win (it took 2nd in category). The sponsoring brewery committed to brewing the winning beer on their system for commercial purposes. My beer wouldn't have been an option in their state without some modification due to ABV restrictions. Ultimately, though, I don't know if I would consider 3rd place BOS losing, but YMMV.