Conjunctivitis that never cleared up

Hello

Back in January I developed a case of viral or bacterial conjunctivitis in my eyes (I had a cold at the time). I would wake up with crusty discharge and my eyes were obviously very red.  

Well it was been quite some time since the discharge has stopped however it seems like my eyes never completely cleared up.  My eyes are still slightly red - what is strange is that the level of redness is not consistent: It is usually redder in the morning and clearer much later at night.  

Any ideas what could be wrong?  I feel that my eyes have never fully recovered and it is causing some concern right now.

Thanks!