What I am trying to achieve; Various content creators are providing me with BVH files with a common bone structure and naming convention. I need to get all these separate BVH files running on a common rigged mesh in Unity 3D

What I have tried; I am using Unity 3.40f5 Standard/Indie with Blender 2.59. I imported an avatar mesh from several .obj files into Blender. Then I imported the a BVH file as an armature, scaling it down to 0.026 during the import. The armature was on his side after import so I rotated the armature 90 degrees around x-axis and 90 degrees around z-axis and moved it into place with the mesh. Then I parented the mesh pieces to the armature (armature as parent) using 'Armature Deform With Automatic Weights'. I then shortened the animation to the desired length as blender seemed to put in a lot of blank frames. Finally I exported everything as an FBX file with the 'Default Take' option unchecked and imported it to Unity scaling it from 0.01 to 1 and animation set to loop. Then I created a new blender file and imported the BVH again as an armature with the same scale and rotated the same way and shortened the animation again. Then I exported the new file as an FBX, this time with the 'Default Take' option on. Again I imported it to Unity scaling it up again and setting to loop. Lastly I dragged the imported rigged mesh into the hierarchy and set its animation to the separate bvh import and tested. Everything played well with the rig now animated. Finally I exported a second BVH file (same bones) through blender as an FBX file and imported to Unity again. This time the animation would not play on the rigged mesh. In fact it would only play on a rigged mesh created specifically with that same BVH file in blender.

My Question is; I have been struggling for over a week to get all these BVH files into Unity and running on a single rigged mesh. Unfortunately my starting point must be the BVH format as this is the area my content creators have experience in. Does anyone have any idea where I am going wrong or could they suggest a better pipeline or approach to get these BVH files into Unity and running on a rigged mesh.