Karen,
I have an eleven year old son who has the exact same problem. I have had him in scouts since second grade and it really helps. He still has problems with the kids in school, but the kids he goes to scouts with help him feel accepted. They have even come to his defense at school. The scouts make him feel normal and admire his gifts of problem solving and his talents in science. I feel scouting is the best thing that has happened to him.
Dear Karen,
Children who are not intuitively social do face a challenge. It's easy for them to be viewed as odd or eccentric, and to fail to establish a circle of friends.
There's a simple goal for you, though. It is to keep your son 'in the mix' - i.e., to be sure, season by season, to have him engaged in some activity of a group sort outside of school. You know the old maxim 'practice makes perfect'? Well, it certainly applies to social relationships. There's no way to learn except to be involved in interactional activities with other children. You may need to do a bit of pushing or gentle prodding/encouragement to accomplish this, but it's the sensible thing to do.