My son from age 9 displayed 'odd' behaviour like nodding, throat clearing, scratching and blinking after exhaustive testing through Dr's psycologists etc was finally diagnosed with Tourettes. Until 9 years of age he was progressing normally at school but then started to slip behind and finally we worked it out that he was so busy trying to control the 'tic's at school so others wouldn't notice he just wasn't concentrating. The Dr's offerred medication...uppers/downers but he chose to deal with it. The tics became so severe I didn't hold much hope of him getting an education or holding down a job but I am happy to say he is now 27 married with 3 children and has a great job and been employed non stop since he was 17. If he is tired or stressed he still 'tic's.
I suggest you see your Dr and ask the question...is it Tourettes syndrome.
Wishing you and your son good luck.
I'm not too sure about the rapid eye movements. When you say "nods his head up and down" is it like jerky movements? If it is, then he most probably has a movement disorder called myoclonus which can be caused by a variety of things but sometimes it can just be benign. You should take him to a doctor to get a check up