Is it a bad case of sticky eye perhaps? Galen had a few nasty bouts of it and needed some eye drops and ointment on a couple of occasions. We kept cleaning his eye (about 6 times a day) with cooled boiled water and I would also squirt breast milk on to it. It took until he was about 4 months old for his eye to actually sort itself out and the tear duct to work properly. Until then it was always gunky, red and never as wide open as the other eye.
Also because his eye was a bit swollen and sore his eyelashes on the outside of his eye were irritating his eye and we kept having to clean them outward to make sure they didn't turn in and become ingrowing. Again, took till about 4 months for this to sort itself out.
What medication did they give for it? And what did they tell you was wrong?