This is standard procedure not only on AS, but on virtually all of the major airlines in the US right now. The benefit is that if you're flying on mile-based upgrades, it'll take fewer of them to upgrade the whole flight. Of course, the drawback is that you lose out on credited miles.

My opinion, I suppose, is to live and learn. If you want to make sure and earn the maximum amount of miles, try scheduling your flights so that you change planes/flight numbers. And this is true for *all* airlines, not just AS.

Mike