LSU beat the Big East and PAC 10 champions OOC that year, rather handily. Alabama had nothing of the sort on their resume, literally their selling point was a close loss to a good team (LSU). Every single BCS computer ranking placed ISU ahead of Alabama. That's because ISU had better wins than Alabama, by several metrics. The only point in Bama's favor was a better loss than ISU had, but it says something when your resume silver bullet is a loss.
The thing that gets under my skin about that is not that it happened in a vacuum. It's that the argument used that year was "But who's the best team?" while "best resume" was used to put Alabama in other years. The voters changed the criteria to get certain teams in from year to year. Saban himself even campaigned on the two different merits in different years when it was convenient (and I don't actually blame him for that, he's the HC, that's what he's supposed to do). If they were consistent it would annoy me somewhat less. But it's clear the voters did what the voters wanted to do and used whatever justification they needed for it.