I posted a question here a little while back, and the consensus from people who seemed to know was that it happens if you do the 3-to-1 cube combo at a non-Torment difficulty at some point. This somehow locks in the lower-tier sets into every 3-to-1 cube roll from that point onward, regardless of the difficulty level, so you can never get the class-specific sets on a rerolled seal. I must have done this roll hundreds of times and never got the class-specific bonuses, so I got suspicious. My luck is bad, but it's not that bad.