I saw that too. Hence the remark about coordinates. I always had plenty of issues with the workflow. It is very fragile. What I saw with your rig:
- The Pivot of multiple meshes is not centered, that may create issues
- There is a keyframe on the rig, That will make changes difficult. Better delete it.
- You can simplify to a single Skin deformer (Select all Skin def and delete, go to char menu and add a single new one, it will take the delted settings into the single new one )
- Your leg joints are perfectly straight. The control rig is confused by stuff like that and screws up Leg Ik. Make a small angle into leg joints
- I wasn't able to apply the Control Rig to your structure as well, constant jumps and distortions. I would redo it with merged mesh and slight bend in knees