Did you visit the teacher about your son reading during lunch? It is possible she is concerned he isn't socializing with the other children,which is important part of childhood development. On a questionier for disability services, a childs ability to socilize is determining factor on receiving a disability approval from Social Security disability. Teachers have training in childrens development, teachers fill out these forms for Social Security Disability. Possibly she recognizes how out of place he feels and her comments aren't negative but actually supportive of recognizeing all of your sons need at school. It is hard for children when they don't fell like they are part of the group. You might find it interesting that in reasearch it is a family that sits down and eats together and talks and shares that time together talking, are the children that do the best. I haven't read research on the importance of children all sitting and visiting and eating together. I provided opportunities for my child to socilize out of school to meet his developmental needs. I shared with the school I recognized he needed support to develop social skills. It helped because the teacher felt I was helping to support her and it addressed the issue where we had the same goal, providing a enviorment to meet his needs.
I also have struggled with going to the school. Have same homeschooling issues.