Silly as it sounds, the Bills changed the helmets to red in 1984 because they felt it would be easier for Ferguson to see his receivers in red, as opposed to white, which the Dolphins and Colts wore. Jets had already changed to green I believe.
Anyways, back in the 80's, the end zones were red, probably to match the helmet. The word BILLS was in blue when they wore blue cages, then changed to white when they switched to white cages in 1987.
And BTW, the end zones and logos were never really "painted".
It was different colored sections of astroturf that was sewn in.