The controls do work but the reason they are not moving with the main global is because they are either not grouped under the global group or parented. You can parent constrain them to the appropiate joint by selecting the joint then the control and then go to the bar menu: Constrain>Parent. Make sure you Freeze the transformations of the control first before you do this, Modify>freeze transformations. Now when you move the root the control will follow the skeleton. You can now group the controls that was constrained to the global group. To do this go to the hypergraph and find the control in there. Middle mouse click it down and drag into the global group to group it under. You do this because when you select the global group and either scale it or move it anywhere into your scene, the attached control will react according to the global transformations without influencing anything else. I really hope this works. When you reach problems like this it's always better to start over and rig it again. It will save you a lot of headaches.