I flap my hands when I get overexcited about something I'm talking about. I also start jumping up and down and giggling sometimes when I'm really excited, while flapping my hands. The other thing I do is "write" words in the air with my fingers, and "type" in the air at times.
I doubt it's a result of hand flapping, but I have horrible tendinitis/carpal tunnel syndrome in both of my wrists. That is from working with my hands a LOT (I'm a very obsessive bead sorter, I make hemp jewelry and embroidery floss jewelry, I draw, I type a lot, etc.), but I don't think my hands flapping around when my tendinitis is starting to die down helps it out much at all, lol.
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Sorry for the long post...
I'm my own guinea pig.