I've used the exact same settings with 7 conference champions auto qualifying for the playoffs.

In the 8 and 16 team playoff setting, the 7 champions all make it regardless of ranking. In the 12 team setting, the game takes the top 12 disregarding the conference champions.

I think I fixed it... the logic was taking the top 4 conf winners and then the next 8 overall. I adjusted it so that all of the auto conf. winners will get in ahead of anyone else.