Thanks jbd and JohnnyH for claryfing the NAUI requirements.
Knowing this, I'm satisfied with the situation, I'd like to let the whole issue drop.
For those who said they would take the issue up with NAUI privately, please don't. I feel this was an innocent mistake, it didn't put my kid in any kind of jeopardy. I have a very good relationship with the LDS, even though I bought most of my equipment from another LDS just up the street.
My Son got the education, passed the required tests, he'll just go back when he's 15 and redo it if we feel the need for it.
This hasn't put him of scuba one iota, he still wants to do all the courses and become an instructor. In the infamous words of a 13 year old. "It'll be cool daddy, I'll be able to scuba for free, teach other folks, get paid, plus I think it'll be a bit of a chick magnet".
Now we are just going to dive, dive dive.
Thanks all.