Yeah this is a bug. Basically what is happening is that when you add substantial artwork like arms or something, you're essentially changing the origin points of stuff like the Head or Body because you're changing its dimensions to make it a little wider or lower or whatever. For some reason sometimes CH doesn't always figure it out and does this instead. Reimporting, unfortunately, is usually your best bet. Thanks for your input - we'll hopefully fix this soon.
Ah that explains it. Thank you for clearing it up Dave. Hopefully it's fix on future update.
I had this same problem, and I even tried to create a large, transparent block around my character in Illustrator hoping that it would keep the puppet in a "bounding box" in Character Animator, but that didn't help either.
Re-rigging a body isn't too time consuming, as much as setting up the head. I though of maybe making one puppet the head and the other the body but that doesn't make sense either... it would be too difficult to coordinate between the two.
Hopefully this bug is fixed in the next version, thank you!