I hope Kalina82 (Kellie) sees this -- her kiddo was having this problem and the vet was saying they couldn't find anything wrong. She finally went to a Vet Opthamologist (who has specialized equipment) and it turns out that (I think) her bottom lid rolls in just a bit and there are microscopic hairs growing inside there, toward the eyeball (I hope I have this right, Kellie!
).
Food can do it, sometimes...can you post ingredients of your food?
Seasonal allergies can also affect this very much -- does she itch or bite/lick her paws at all? You could try childrens benadryl to see if this helps w/ the eyes.
Usually when it's an eye infection, you see greenish goop and there is usually a smell to the eye area.