Can I get some assistance with " motionmapper.exe"?

Can anyone help me or tell me what I am doing wrong? I understand that you take your skeleton mesh you want the animation to be on and the animation from the valve characters to generate the new animation. The thing is any time I use " motionmapper.exe" to generate the new animation, the animations do not come out the way they should. The last time I did this the upper torso was at a 180 degree angle and not flowing to the animation. Any help would be greatly appreciated.

Can anyone help me?