Would you consider UF the undisputed champions? Boise State was the only undefeated team and actually received one first place in the AP Poll. I'd claim that in this century the only undisputed national champions have been us last year and Ohio State in 2002, because both teams received all of the AP votes, won the BCS, and the BCS game was clearly 1 vs. 2.
Here are the controveries:
2006 - Boise State is undefeated
2004 - Auburn is undefeated, left out of the game
2003 - USC wins the AP poll, LSU the BCS
2001 - Nebraska doesn't win the Big 12 but plays in the MNC, and Oregon feels left out
2000 - OU plays FSU, even though Miami beat FSU earlier that year and was ranked # 2 in the AP.