I just installed an Undercover Armor flex, and mine was similar. The youtube install videos I watched said to give the top rail a good smack while tightening the clamps during install to make sure they are sitting flush with the bed rails. When I noticed it was uneven I went back and loosened the nearest clamp a little, gave the top rail a good whack with my hand, tightened it up while applying downward pressure, and it seemed to work. All even now.