http://i.imgur.com/bcu9T.png
Comparison of messed up vs. normal.

Reloading doesn't fix, quitting and relaunching does. Not sure what's causing it. My mod list is pretty short and simple, and doesn't include anything specific to eyes.

Minor issue but an annoyance nonetheless.

Seems to be linked to the invisibility spell.

Try typing in the console "sixchange" twice. That should fix it.

I had this issue as well.

I get it too on a female khajiit, always the left eye.

You might be onto something with invisibility. Shadow Warrior seems to be the trigger for me too