this is called stickyness and has to do with IK setup. when you create an ik handle you can check stickyness, which means basically that the ik handles stick to their point in space unless you move them around. you can create ik handles without stickiness checked but after the first keyframe is set they become sticky again. in case you want them handles to follow the rootnode simply group the whole hierarchy and use this null group as your new rootNode.
everything starts and ends in the right place at the right time.