Don't know if this is the right forum for this but this caused some confusion for me atleast. It is an error in the Helpfile that is the cause of confusion.
Under the helpsection on the Characterize tab.
The section about reference
"Reference
While you do not need a Reference object during the mapping process, this slot lets you define an object to act as the root of your entire character. This object lets you translate, scale, and rotate your entire character. The ideal reference object is a joint or locator parented to your characters hips."
You are ofc supposed to parent the hips of your character to your reference object. Not the other way around.