I am glad I found this post! I am currently going through the same kind of thing...the GI doctor found 3 or 4 areas of inflammation throughout my tract but the biopsies all came back as normal and self-limited. I guess it does go to show that sometimes it takes time to find out, unfortunately!
It is confusing, too, when the GI doctor thinks you are ok but your internist does not...I really need to ask my internist what's next??