It's making me think of crohns disease too but there's a lot of different possibilities. I would see a different doctor (like JGF25 suggested) as soon as possible. Poor thing. A friend of mine has Crohns disease and it took a while for them to finally come up with her diagnosis.
I think it is time to see a gastroenterologist. A pediatric one if there is such a thing. There is a reason for specialists, and this is the time to see one. Good luck and I hope she feels better soon.