My son (5 at the time) had ZERO symptoms and his drastic change in behavior was the thing that brought us to the pediatrician. (Strangely, I had all the classic symptoms but had never considered Celiac Disease.)
He went from being a well behaved boy (no angel, but certainly within manageable limits) to someone we hardly recognized. Tantrums lasting hours (over the smallest thing), meltdowns over common frustrations (putting on socks) and a lack of interest in things he formerly enjoyed ("everything is boring") He used to rush home to do all his homework, suddenly it was a struggle - ending in a tantrum or meltdown. Consequences didn't matter, reasoning didn't work, it was clear he was not in control of his behavior. This went on for several weeks. We got to the point where we didn't want to take him anywhere because his behavior was so unpredictable. Strangely, the teachers at school (Kindergarten) saw NONE of this and were shocked when I described his behavior. He was somehow able to keep it together at school, but not at home.
After about a month, he had three days in a row where he complained of a stomach ache. Then they went away.
I had already made an appointment with the doctor so we went and she couldn't find anything wrong with him. When I mentioned the terrible behavior we were dealing with, she thought to give him the blood test.
He was positive on some, negative on others. His biopsy ended up being very positive.
He was back to his usual self within weeks of being gluten free and now we see the tantrums only about once a month (cross contamination? Not sure. ..)
I know this is an old post, but I feel like I could have written this exact post! We are just starting the testing process and I am researching like crazy. You say he tested negative on some and positive on some. Would you mind sharing the tests he had done and the results? Only thing so far my son has had is the tTG and the total IgA and they were both negative.