Consider seeing a vet, Check carefully for mites, they attack the eyes typically. They will look like little specs of pepper, either black or red.
Could be an infection,clean with a q-tip and more vitamins to the diet, typically animals dificient in vitamin A and C have reoccuring eye and mouth infections.

Could be an alergic reaction, are you using pine,cedar or some other bedding that could causing a problem? Do you use incents or other such products?