Ah okay. Though it's your adopted kids that are getting the yellow eyes I thought I read? That maybe harder to reproduce.
I just thought of something the game maybe getting the option from though. When you create a Sim do you save your eye/hair colors? If so, it may be picking from that?
If you think that might be part of the issue. You can delete the
userPresets.package file which can be found inside your documents\Sims 3 folder.
It won't delete your CC patterns. Just the colors/textures you've saved while in CAS and CASt. If you'd rather, you can cut and paste it to your desktop.