winning would help their conference and they have a slight (maybe even subconscious) bias toward that team? Would officials call penalties (or witheld calling penalties) that favor the team that stood the best chance of making a national splash and helping out their conference? The fact that these teams could possibly rake in a lot of money for the conference if they go to a big bowl isn't something to be ignored.
I am NOT saying this happens, but rather that money and power in the world of sports have led many to abondon ethics. We see it every day in the headlines.