Given the amount of training he does, have you watched him run or cycle? If he pulled his hamstring some time ago and returned to training very early he may have developed compensatory patterns to protect the injured muscle, which have become habitual.

There was a thread recently discussing in some depth things to look out for on the bike - video the athlete from the back and the side and see what you can see. In my experience with triathletes, very often their main complaint is pain when they run, but more often the underlying problem is on the bike, on which they spend a great deal longer than they do running.

A minor biomechanical issue rapidly becomes a major problem when someone is putting in serious hours and miles on the bike, especially if they are doing hill training.