It's happened to me too, but with default sims (the Roth children that come with either Seasons or Bon Voyage). For the life of me, I can't find makeup for the eldest girl, now in college, it always seems like her eyes are too high, or her cheeks too low, leaving a large gap and making eyeliner and eyeshadow look like they were applied to her under eye. It looks weird but I thought it was just a problem with this family. Only after I saw that other thread, I could see that more people are having the same problem.
I've been trying to stay away from using too much 'plastic surgery', resorting to it only in the most extreme cases. But I might need to start from scratch with her and use a template face to fix it.
The next kid, Xander is about to enter college and his face is not so bad, but they've got a fresh set of twin girls who might also be candidates for the sim blender (my knife of choice).
I'll be looking out for any solutions posted for this thread or the other one, from the more experienced simmers around.

Mari
