It's most likely due to anxiety..
I'm not really sure if this could help any, but maybe make a fun little game for when he gets this way to where he can run as fast as he possibly can, with a goal or record time setting or something? sticker achievements?
quite honestly, i dont realize things like this until AFTER it's been done(tho on other times i can catch it before. like when i'm out in public i've pretty much been able to not cover my ears, but sometimes i still catch my hands going up towards my ears to cover them. and then i feel all awkward and even more nervous).. it's more of an instant full dose of adrenialin/flight scared kind of feeling. and for me it's not always anyone else can see, like i can be in my own little world, and going throughout my memories of the previous day and then something i didn't realize before that my actions or words could of been commonly taken/mistaken as, i go into a quick panic type thing, but usually i am home when this happens, so i usually in an automatic reaction shake my head, and shake my hands (sometimes they pop. it's not an intentional thing tho). growing up people would assume that i would be doing this to either get attention, or self harm on purpose. but none of it was intentional... ... I dont know if it's the same for him or not.