Quote Originally Posted by Frontier View Post
It's his ego and obsessiveness.

He's absolutely brilliant but he still has personal foibles and issues that get in the way.

Just like Riddler is probably smarter then most anyone but he can't help himself by leaving clues that end up getting him caught.
Like Lightning Rider said, there are different kinds of intelligence and this is clearly the subject where Lex would be stuck in the remedial class.