It could be iritis (aka uveitis) which is part of the auto-immune UC disease along with arthritis and the like.
I've never had it but my well-informed family doctor told me about
it. Perhaps your eye doctor isn't up on UC related eye problems (but should be).
And your GI doctor of course should be suspicious of the connection. It's treated several ways including steroid eye drops.
Here's info on it:
www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002000/If you do have iritis and your GI didn't pick up on it that's not a good doctor IMO.
I have no experience with Flagyl so can't offer advice there.