I have the same problem.
I've downloaded a sim from the gallery. Then i tried to modify him in another different sims,and they live in two different houses, only with slight modification on the appearance and name. I saved both in the gallery with other names and appearances. First i introduce to the game the unmodified sim, but when i introduce the second sim slightly modified in the game, that has been modified from the original one, he suddenly changes in the original sim, so i have the same sim in two different houses but only one playable 'cause the game read him as the same one, so the original disappears from his family and his avatar pic. became grey. It's like the game thinks he is the same,so erase one and changes the appearance of the other to an unmodified version. Maybe, also if you modify one sim in CAS, it doesn't change some code and for the game is the same sim. Don't know, but is rather unnerving, because almost always I use the same base sim to modify into other. It's actually impossible right now.
