read this forum topic for more info:
http://blenderartists.org/forum/showthread.php?260602-transform-matrix-to-bone-%28head-tail-roll%29-bug

So for the time being it's not possible to get a model from many formats to Blender and export back, without modifying it's bone values, if those formats use bone matrices.

So we can't use Blender 2.6 to modify models in such format made with the older version of Blender or other 3d modeller, without it breaking *all* the animations already made.

On top of that, the Python API has no function for this and we had to dig in the Blender source. The old 2.4 API had it. So please bring it back?