A vaccine isn't always going to be 100% effective. Our vet recommends we change which pinkeye vaccine we use about every 2 or 3 years because he feels once the same vaccine has been used in consecutive years it becomes less effective after that so switching brands every so often can make the vaccine more effective. It's kind of like the flu shot for humans, just because you get a flu shot doesn't mean you are 100% immune and won't get the flu. There are different strands the vaccine may not be effective against plus pink eye can also be a result of the environment the animal is in. Seems like when you get drier years is when you see more of it because the dry air and dust seems to cause more eye irritation.
I will say that for the longest time we never vaccinated for pink eye and just treated it on a case by case basis but then had a really couple bad years of it when we had 2 dry summers in a row and have vaccinated for it ever since then and had very few bad eyes to treat. Seems like Herefords with less pigmentation are the ones that get it easier than those that have noticeably more pigmentation but to show you how environmental factors can play a factor the neighbor just down the road from us runs mostly black cows and the same dry year we had pink eye problems they had one of their black bulls nearly go blind he got it so bad in both eyes. They had to pull him from the pasture because he was running into things and they could tell that he didn't even know they were walking up to him.
