M.P.
That has happened to my son every year also! Last year it worked out great as he made his best buds. This year he has a whole new group. He hasn't found great buddies but I think he is just the type to have a few close friends-not a ton of acquaintances and thats OK. Our kids aren't allowed to mix up tables at lunch either but my son does anyhow. He either just sits with his friends or they all sit in the nut free zone. I am not going to condone this but I am also not going to tell him not to. If he gets caught then he has to deal with consequences. I am actually kind of proud of him for "working around" his situation.
Since your son gets along great with all the sports teamates could it be that he is so disapointed in this class that he is not trying to make friends? Maybe you can talk to his guidance counselor. Ours will take a group into lunch with her to either mediate or help kids get to know eachother.