My DS7 went through this terribly last year in kindergarten. He was crying most nights at bedtime and saying very sad and scary things to hear from a 5 year old. We talked to his teacher and got the school social worker involved. They were fantastic in helping him work through the issues he was facing doing things such as hooking him up with a recess buddy, going out on the playground at recess to see what was going on and offer help and support and letting him bring out special games or toys from their stash so there would be a structured way for him to interact with the other children. While he didn't develop a best friend, he felt much better and was interacting with the children more. The crying at night stopped and sad thoughts, too. This year has been up and down, but it has been much easier than last year for him. We met with his teacher before the first day of school to give her a heads-up and so she could be proactive with him. When he started to have the sad thoughts and feelings again this year, I didn't hesitate to contact the teacher and school social worker. The social worker would meet with him once a week to talk about friends and issues, and she started a "friendship club" with three other first graders who needed a little extra help with social issues where once a week they got together to talk about being a friend, played games to practice social interactions, etc. my DS loved it, and I think it made such a huge difference for him. He still doesn't have a close friend or someone he feels has the same interests as him (still feels different) but I think he is much happier.
As to your question on the cause, I think it is a combo of things for my DS. But in the end, it didn't matter so much to me the reason or even if it is a normal development thing for children. I saw my DS in such emotional pain that I knew I had to do something. Trust your gut on what your child needs.
