The exported hierarchy was the Kinect v2 hierarchy when it should have been Kinect v1 hierarchy. In addition, some of the spine orientations were computed incorrectly with the libfreenect2 flag enabled.
The hands are included in the BVH hierarchy with the Microsoft SDK (and in this cause, with libfreenect2 due to the bug) even if they are disabled. This was left in mostly because it didn't really cause any harm - the hands simply are at rest pose, inheriting the orientation of their parent bone.
We have the fix ready, and hopefully can push out 2.14 on Monday after the testing finishes.