what causes "stemming" or wrist flicking in Autistic children?

I'm curious what causes austistic children to flap their wrists?  I ask because my son is 2 1/2 and he exhibits wrist flapping - he's been doing it for as long as I can remember.  Developmentally however, my son is terrific.  I do not believe that he has autism - or even aspergers.  But the only children I have ever seen flapping their wrists like my son are children with problems such as autism, fragile x, and other developmental problems.  So, what causes this?  Is it neurological?  Could my son have a neurological problem to children with autism, but not actually have autism?  Also, when my son was being breast fed (1 month) he was fine.  When I put him on similac he began crying ALL the time.  And he would cry for HOURS.  Finally, I switched his formula to carnation good start, and he improved almost immediatly.  When he began eating solid foods and drinking milk, he started having problems again - including extreme diareha.  I took him off regular milk, and he is better again.  The one thing that regular milk and similac have that good start and his new milk don't have is casien protein.  I know that it has been said that autistic children have an allergy to casien - is it possible that I have not completely removed the casien from his diet and this is what's causeing the wrist flapping?  My doctor said it's normal and if it doesn't go away in 6 months she would look into it.  That was a year and a half ago - she still says it's normal, not to worry, but has never pursued an answer.  What should I do?