I can't speak to involuntary cross-eyed-ness (???), but I know that it is good for eyes for people to choose to go cross-eyed. It strengthens the muscles. Contrary to what moms used to tell kids, your eyes won't stick that way in real life (normally!).

Now, why they are staying that way for your son, I'm not sure. I'd definitely talk to the doctor about it--not just the assistant!--and pronto.

Kriston