Fun fact: The same two schools which were college football champions in the U.S and Canada for 2009, Alabama in the NCAA and Queen's in CIS, also won it all in 1992.
Now, the punchline: in 1992, Boise State had not joined the NCAA's top division. They call Alabama the Crimson Tide, but "Steely Dan" Brannagan and the Queen's Golden Gaels were put through a true post-season. Times change and so should the NCAA. That is all.
Shockingly, Boise State Is Dissatisfied With the "Fundamentally Flawed" Status Quo (The Sporting Blog)