I added a control rig to a character and for some reason the neck and head of my character got squashed. It somehow has modified my original skeleton (a couple of nodes, specifically the head/neck are moved). The skeleton shows a green validation of my definition under character controls. This a skeleton from the autodesk character generator website with a different mesh added. When the new mesh was added I did adjust the skeleton to fit and then deleted history and froze transformations. The character has been brought into motionbuilder and had animations retargeted to it with no problems or any control rig added.