Not exactly, then it would be easy, because I could at least pin-point it to the follicle workflow. In the test scene I also used my script to attach the CVs to the bones via follicles and it just worked fine for me. So that's the thing that confuses me so much.
The way I attach the CVs to the follicles is, that I take the transformations of the start and end follicle and pipe it into the cv[0] and cv[1].
I can upload the test and muscle scene for you, so you can have a look at it.