Maya to Unity - joint orientation ignored or lost

Update: This question is related to this topic: http://forum.unity3d.com/threads/129987-Maya-to-Unity-Joint-orientation-ignored-or-lost-on-import

Original I am currently rigging a vehicle with lots of mechanically moving parts. Joints are a requirement for this project (GDD demands, programming demands) - so no, cannot do this in Unity.

The joints have been setup and skinned to the appropriate mesh parts in Maya and every flap, under carriage etc. is swiveling nicely around its hinge axis in Maya. I am doing this by adjusting the jointOrientation and zeroing out any rotation of the bones (so the neutral state will be 0) - so in the end I can rotate a flap around one of its local axis.

Exporting to fbx. Importing into Unity.

In Unity some of those joints work like a charm while others completely ignore the joint orientation. I am testing the flaps by dragging the prefab into the scene and rotating each of its hinge bones. Some are using the joint orientation given in Maya. Some are using the local axis of the root/object instead.

What am I missing here?