Well, I didn't try Serana but now I do and her eyes are missing too. It's a good thing that you posted a screenshot. What I see here, is that you use copies for the eyes. I don't know if you have your own copies of the nifs and textures as well. But I begin to think that there's just something wrong with the NIF files from Bethesda itself. I have no idea how to fix that, however I'm sure someone else will be able to fix this. Should be an easy fix, all eyes work correctly ingame.