Third eyelid

The third eyelid of my cat is more noticeable lately. It is covering about a third of her eye in one eye and about a fourth in the other eye. She has no other symptoms of any illness. The third eyelid was red, but since I started putting anitbiotic ointment in her eyes (as my vet advised), it's not red, but the condition isn't improving much either. She is also squinting, the squinting has gotten a little better with treatment.

Does anyone have any insight on what might cause this, or what might help this?

I've read some stuff on conjunctivitis, but I'm just not sure about what might be causing this. The viral conjunctivitis symptoms don't seem to fit. I even saw pics on the net and it looks nothing like viral. But, if the antibiotic ointment isn't working very well, what would it be? How or where would I start to narrow down the cause? Could it be allergies? What kind of things are cats allergic to?

I've been using the antibiotic ointment for 48hrs. Is this long enough to see some results of it getting better?

Maybe it isn't even conjuntivitis, are there other eye conditions that could be the cause?

third eyelid can mean a lot of things:
fever
dehydration
infection
eye irritation
Horner's Syndrome
elevated third eye (genetic)
cornea is scratched