Animation on 'extra' bones missing/stripped in Unity. (Unity 4.6)

Our skeleton has a number of bones which are not included in Unity's Humanoid Avatar definition. Extra face bones, and a couple of joints used to locate/animate props like balls or other characters.

On a previous project the animation on these extra bones would be retained if they were included in an avatar mask. But now on Unity 4.6 (possibly earlier) this animation is gone. The joints remain in their default positions.

I have also tried switching the rig to generic but then all the animations appear to Tpose.

Thoughts?