What I do to fix this is go to armature edit mode, add a bone and place/size it to where hips is, and reparent the bones that belong on hips and rename it to "hips" or whatever the name of the base's bodygroup has (sometimes lower case, sometimes capital, depends). I'm guessing blender treats the original Hips as the armature container and kind of break it, but this seems to work for me.