The only thing I can think of is 1) have they done blood work to test and make sure he's getting all the nutrients he needs?
2) Have they checked his heart? My niece had a problem where she would pass out and have small seizures (it only happened a few times) and it turned out to be something easily fixable with her heart. It gave her headeaches and made her tired, and also caused her to get dizzy. She was 13 when she started having problems. She had to wear a heart monitor for a day and had some other tests done. An EKG showed nothing, but this was the only thing they could think of.
3) Push and push and push for an answer. If this doctor can't figure it out, get a new one. It could also be more than one thing adding up, and not all the same problem.
4) Have they checked for nerve related issues or for anything in his brain?
Has the doctor or a nurse ever seen one of his seizures? I know this is going to sound crass, but if you can catch it on video that might help. Also, try getting him to keep a record of what he eats, what he does, where he goes, his pain levels, spasms etc, it wil lbe ALOT for a 12 year old but it can't be worse than what he's handling now.
This is the best I could come up with, but I wanted to reply. And *hugs to you* and him, take care, and please please, if nothing else, check back in with us so we can help you through it, even if we can't make him better.
"When we come to the edge of the light we know, and are about to step off into the darkness of the unknown, of one thing we can be sure; either God will provide something solid to stand on... or we will be taught to fly.'"
"Cause when push comes to shove You taste what you're made of, You might bend, till you break Cause its all you can take; On your knees you look up Decide you've had enough, You get mad you get strong Wipe your hands shake it off, Then you Stand" From "Stand" by Rascal Flatts
Dx.: Polycystic Ovarian Syndrome, Ulcerlative Colitis, Chronic Inflammation of the Colon, Ruptured & Fused L4-L5-S1 w/pinched nerves, Degenerative Disc Disease, Chronic Costochondritis, Back Muscle Spasms, Asthma, Benign Tremmors (hands)