http://www.ncaa.com/history/default.aspx?id=91434
They are recognized as the consensus national champion in 2003.
They say on their website that they do not recognize FBS national champions. That's why they have it broken down into FBS and have the column, selecting organization.
http://www.ncaa.org/champadmin/champs_listing1.html
This is the official NCAA site for champions won and if you notice they dont count FBS Championships, just I-AA, DII, and DIII