Declan without any more information (specially the files) it would be hard to say why it is not working. Any chance if you can upload the files?
Please check #18 of this post on how to upload files: Forum Posting
are you animating or are you doing motion simulation?
if you build a brand new motion study and just control that one mate, does the same issue exist?
when you post further info, can you include some screenshots and a step by step on your workflow? i'm not totally following based on the language that you are using and the pictures may help a lot.