Thanks everyone for all your feedback.
The reason that I've mentioned the "skip" as a possible reason for attention is that even though "we never mentioned it" to students/parents at the school. They all figured it out quickly. A year later, I still have people asking me about it. I usually just brush off the subject because the questions feel very invasive and pointed.
The way that I see my son stand out is that he doesn't seem to want to be in the middle of a bunch of kids. He has always been a little crowd adverse. So things like recess bother him, and he will just stand out of the group. But then, he feels left out and not included.
The other thing is that he has a low threshold for aggravation. It gets better ever year. This school is probably worse in a way because it is a little less structured than public school. He is more of a rule follower.
He is good with social queues (facial expressions). He is polite. He likes to greet everyone.
He loves to read. So, he always has a book in his hand. He really wants to find someone to sit and talk about books with him.
