Blendshape made in Editor works in Scene but not from a Prefab?

Hi There
I have a system that makes Blendshapes on an Skinned Mesh in the Editor and it works I can add just what I need and they work perfectly, I can copy the object and the Blendshapes work just fine etc. Problem is when I make a Prefab out of the GameObject using AssetDatabase CreateAsset, SaveAssets, Refesh from script the Prefab gets made just fine, the mesh and materials all work, I can drop the object into the scene and it appears but when I change the BlendShape slider the meshes just messes up.
Is there some special trick when making a Prefab from an Object which has Blendshapes that were not present in the imported model. Below is a screenshot showing the Blendshapes working just after they were created and then the one below that shows the Prefab object with a Blendshape slider set.
Can anyone help?


After some more digging everything works fine if I turn GPU skinning off, so it seems like there is some internal mapping of vertices that is not getting set.