Awww...poor little thing. I can imagine that is extremely uncomfortable. What drops are you having to use for him? Can you give the names of the medications?
These things can be caused by many different things...it's almost impossible to tell most times. (Unless it is viral, which they detect with the stain that Nancy mentioned.) It will most likely get better, so long as you keep the area clear of stray hairs and such and keep up w/ the drops.