When I save my artwork in AI then open Character animator

I've not encountered this problem in a while, though it's not unheard of. When I encountered it, it was because I had done something to the original that would throw off the alignment, such as change the dimentions of one the objects by removing something. When that happened, I really had no choice but to drag the affected parts back where they belonged (or in more drastic situations) re-rig the entire character. I do not know if this problem has been addressed or if I've just gotten really good at avoiding it. In case it's the former, check to see if you're using the latest version of CH. If you're feeling adventurous, download the beta version of the app, since they are fixing things practically every day.