Hi Sean,
Have you enabled “Auto Save”? Is there a file with the state you liked, and can compare it? OR even better that works as you wanted it ...
The main thing normally, and described in all books to my knowledge is, that the orientation of the joints are not good. Could it be that the orientation of the joints has changed?
If you move arms, head and legs separately, is all “messed” up, even parts that weren’t involved in the C-Motion set up?
The next thing I would check, are the poles and targets (if IK was used) in a “working position”. Does the Pole object provides a good 2D plane?
I can’t see a change of the weighting with the C-Motion, hence why I exclude it here.
Let’s hope you have a back-up and can compare, at least.
My best wishes