Is it possible that he just does not have a lot of male influence in his life? If I am way off base please excuse me. If you think this may possibly be a cause try big brothers and/or boyscouts. Sometimes one on one guy time helps. If he is happy and well adjusted I would not be too concerned though, he is young after all.
My youngest son was like that. He did have boys who would attempt to be his friends - and he was well-liked, as you say about your son, but my son didn't like competing physically, and didn't like playing rough sports. So, that left him completely without stuff to do with other boys. They wanted to play airsoft, or wrestle, or football, or other things where there was a definite winner or loser, and he was always on the loser side. : ( It's funny, he hikes the canyon all day, explores the woods, rides his bike forever and is trim and fit, but as far as competing strength-wise, he just couldn't do it, and didn't want to.
He's turning 13 next week and his friends have completely changed. He has a regular crowd of 6 neighborhood boys, and more aquaintances who all get together every weekend or so for some activity.
I don't know what to say except wait it out. And keep thinking of things other boys might want to do - action movies, a trip to the creek to catch tadpoles, etc.
Best wishes.