Contacts are good to have. I have found that you, at the very least, need contacts of all the default eyes (or default replacements) plus the alien eyes. Every once in a while your 1/2 alien sims will give birth to a baby with a normal skintone but no eyes. They get the alien eyes in their DNA, but since they don't have the alien skintone (which is necessary for the alien eyes to show up) they get whatever eyes are painted on their skintone. There is no way to fix it other than just give them contacts, since their DNA is NOT messed up like sims who have had their custom eyes deleted by you. They just happened to get empty holes for eyes because Maxis didn't test the game enough.
I had a similar problem but not as bad. I tried out a number of default replacements, and one of them (I think it was Helaene, or maybe Louis) stuck itself on the CAS templates. I mean the head displays in CAS when you are choosing hair and whatnot.
So the heads in CAS still have those eyes, but all my sims show the new defaults. In my search to figure out what the heck was going on, I deleted a heap of eyes, and then some of my sims ended up with the damn annoying default eyes. Again.
This problem has persisted through installing a new EP, which I thought might reset whatever the problem was with CAS.
Most likely your thumbnails cache has simply not updated. Either empty the Thumbnails folder in My Documents\EA Games\The Sims 2 or go into CAS and hold down CTRL and right-click on each thumbnail to refresh it.