I've spent the last week trying to combat this problem myself. I've repaired my game, I've uninstalled and reinstalled the entire game and all expansion packs. I have NO MODS or anything non EA installed in my game. This issue became prevalent after I installed the vampires expansion pack.
I created a sim with white hair and black eyebrows, after I save and close the game and come back her eyebrows are also white. When I do the full edit cheat to change it back and check my settings the box for matching hair and eyebrows remains unchecked. I fix it, check ALL forms and outfits, and close. Her eyes brows STILL match.
