My DS1 constantly had gunk in his eyes when he had a cold of any sorts. I used to take him to the Dr's & treat him as if he had conjunctivitis so he could go to day-care, but I was never convinced he had it. In the end our GP sent us to an eye specialist & when I explained the situation she believed the same as I that it wasn't conjunctivitis his nasal tubes were just too small still to cope with the mucous.
For conjunctivitis his eyes will be red, itchy and crusty when left. It will take a little while to clear up with the drops. While in our case with a normal cold the mucous would clear straight away from the drops. DS1 had conjunctivitis once at about 13-14 months & I knew it was different to usual. It took until he was 18 -20 months for it not to come out of his eyes.

Sorry not much help on how to tell the difference but just wanted you to know that we have been through similar.