squinting kitten

Reuben is a 5 month old kitten and was taken out of an old barn about a month ago. He was cover in fleas and had ear mites but otherwise looked pretty healthy. He was given treatment for the fleas (revolution and capstar) and dewormer (pyrantel) and has since been vaccinated against rabies and distemper. He also tested negative for FIV and FeLV.
 
He spent the first week to week and a half at a shelter. He was in a room with one other caged cat that was battling URI but everyone was careful about avoiding cross-contamination. He had no health issues at the shelter once the fleas died off.

I took him home with me after the fleas cleared up and that was when he started squinting his left eye. There wasn't any discharge and the eye didn't  seem to bother him otherwise. A few days later I noticed a little bit of sneezing so when he went to the vet for his shots, we also put him on a two week course of Clavamox drops incase he had caught a URI from the other shelter cat.

He finished his last dose of Clavamox a few days ago, and last night we notice he's squinting again but now he has switched eyes and it's his right. Both eyes this morning has some goopy discharge in the corners near his nose. The discharge is a cloudy off white to light yellow but not green and doesn't really look like infection goop.

I cleaned the eye and had a warm compress on it this morning but it didn't really seem to make a difference.

We had some company over yesterday (before the squinting started) for maybe 2 hours and he was a little stressed at first but warmed up to them and was playing with them before they left. 

I've thought maybe he has herpes virus and it flared up when he came home with me and flared up again when people came over. The only other thing I can think of is that I also have a rabbit in our apartment and maybe something related to the rabbit (fur, hay, etc.) is causing some sort of allergic reaction?

Does anyone have any thoughts? He has no other symptoms and since it's switching eyes, I'm not over concerned that it was a corneal ulcer or scratch.. he also doesn't really rub his face excessively. I'd hate to put him on more antibiotics if he doesn't need it.

Sounds like he's got conjunctivitis, which is an eye infection.  I'd get him to the vet for some eye drops.  The discolored eye discharge indicates something is going on with the eye.   It could also be that the upper respiratory infection didn't clear up completely. 

I checked the conjunctiva in both eyes this morning and there's no inflammation or redness like you'd usually see with conjunctivitis. Nothing going on with the third eyelids either.

The discharge has a slight color but nothing that really screams eye infection. It looks more like the human equivalent of "'morning eye gunk" or what my dog would get from spring allergies.

There's no other symptoms and he isn't consistently squinting either. One minute both eyes are wide open, next minute he's squinting one.

He has me stumped.

Clear discharge is okay, but anything colored is not. It could be anything from allergies to an infection, especially since you mentioned that he'd recently had an upper respiratory infection. 

I bought some genteal for the time being to see if that clears up any irritation with the eye.

We were overly cautious when we put him in antibiotics. He really only sneezed like once or twice but since the eye was squinty and he was at the shelter when there was URI there, he went on meds as a precaution to stop anything that might have been brewing. There was never any congestion.