Hi,
This issue was resolved in MotionBuilder 2009.D patch.
The fix is also documented in the MotionBuilder 2010-Resolved issues section of the documentation:-
Setting the Base Layer for Animation Layers in Python
It is now possible to set the base layer for animation layers using Python, following changes to these methods in FBTake: SetCurrentLayer, SetLayerName, GetLayerName, GetLayerCount, RemoveLayer.
If you require patch for MotionBuilder 2009, you will need to have an active Gold subscription support contract and contact the Autodesk support team as I do not think it is publicly available.
Regards,
Lee