This sounds a lot like my situation right now! I have had Episcleritis of the eye for months now--since June. It was in both eyes, cleared up about a month ago, and is back in one of eyes. Anyhow I went to see an Internist after going to the eye doctor for months and she said Crohn's causes it in many cases. Anyhow I have been through the blood tests--all normal, had upper endoscopy and colonoscopy and both came back showing inflammation in several places, but the biopsies could not link it to either Crohn's or UC. My GI, based on the letter she sent out after my procedures, does not believe I have IBD but my internist does and believes I am in the early stages of it. She says that it can take a while for Crohn's to positively show up in biopsies, and I had another patient on this forum tell me that they heard it takes on average about 5 years to diagnose Crohn's. In addition to the eye issue, I have had other symptoms as well--rectal/anal bleeding, sometimes so bad I was not sure if it was really my period or not (turns out it wasn't), I get the mouth sores, apthous ulcers or whatever they are, I will get awful diarrhea and stomach pain. Sometimes it hurts to eat and I feel better--but very tired--if I don't eat.
I really hope they are able to help you out soon! It is so frustrating to know something is wrong and not have anyone be able to diagnose it. I would not wish Crohn's or UC on anyone! At the same time, I would like to know what is going with my own body, even if it meant one of the above.
Best of luck to you and keep us updated!