A.C.
Another possibility is food allergies. Our now 4 year old used to throw up on a daily basis when he was younger, but seemed to have gotten better, though he will still just vomit at random times. Due to eczema and asthma, we decided to have an allergy test done about a month ago and were shocked to find that he is allergic to chicken and eggs. These are two things that he has eaten all his life (since he was allowed to eat those things in normal guidelines) and we never had any idea, since he didn't break out in hives or have problems breathing in a normal allergic reaction kind of way. He would usually throw up during the day, but it definitely happen at night time sometimes too.
Good luck. In any event, I would push for a second opinion.