I applaud your approach to your son's behavior. It is good to take a wait and see stance with children's behavior and not get too worried about things. When his behaviors and/or anxiety start to impact areas of his life, it is time to intervene. If his hand flapping is affecting him socially or his anxiety is effecting him academically, then it is important to do something before other difficulties start to develop. You stated that he is an anxious, over achiever, this is part of his personality that he will carry all of his life. Skills he learns now will help him all of his life. I would not jump to medication, I would look for a therapist/psychologist who works with children. Your son can work with this person to learn skills that will help him manage his anxiety. You and your husband can learn how best to support this skill building. Like you said, telling him to stop only makes it worse. It makes him more anxious and the best way he knows to manage his anxiety is to flap his hands. Seek professional help, anxiety is very treatable.