The widespread belief on campus was that Lowder exerted tight private control over the Board, and thus over the ostensibly public university, using his clout to place some of his close friends in positions of power.

[8][9] In 2003, when then-University President William F. Walker and athletic director David Housel secretly spoke with University of Louisville football coach Bobby Petrino about taking over Auburn University football coach Tommy Tuberville's job, it was Lowder's private jet which they flew to Louisville.

[10] In the Spring of 2011, Alabama Governor Robert J. Bentley was the decisive vote on the five member nominating committee, which chose to re-appoint Lowder for another twelve-year term on the Board.

[11] Following this vote, a former alumni association president, Andy Hornsby, filed a civil lawsuit in Lee County Circuit Court, claiming that the appointment violated the state's Open Meetings Act.

Lowder's tenure on the Auburn University Board of Trustees ended on April 10, 2012, when the Alabama state senate voted to replace five of the fourteen members.