You might still want to have her checked for Crohns Disease. I had never heard of young children getting this but my brothers granddaughter was recently diagnosed with it and she just turned ten! She probably had it for quite a while before she was diagnosed too because they kept testing her for other things and ruling them out one by one.
I don't know how young these symptoms can show up, but my daughter had stomach pains and nausea for years when she was a kid, and was always extremely thin. She would be hungry but then had to stop eating after a few bites because of stomach pain, followed by nausea. She ended up eventually being diagnosed with severe acid reflux and a hiatal(?) hernia, which was repaired with very minimally invasive surgery ... tiny little incisions between her ribs. Hers was originally misdiagnosed by a &%$#! local "physician" (known around here as one who is not aware of his own limitations!), which delayed things. But when she was 19 she finally went to a Gastroenterologist who diagnosed her correctly and did her surgery, and she is much, much better now.