I saw this on the LSU Tigers Wikipedia page. The NCAA does not count BCS titles towards total NCAA Championships.
"In 1998 major Division I-FBS conferences came together to created the Bowl Championship Series in an effort to establish a more legitimate national champion. LSU won the 2003 BCS national championship and the 2007 BCS national championship. These are not NCAA sanctioned national championships, and because of that, many members of the sports media and fans still refer to them as Mythical National Championships."