I honestly think the problem here is with the scale-on-export. I know that’s what was recommended during the Blender Twitch stream, but since 2.73, I’ve had problems any time I tried to use scaled output with Blender’s FBX exporter on a skeletal mesh.
I’ve had better luck with treating Blender units as centimeters, making sure scale/rotation/location are applied on both the armature and mesh, and ensuring that the root node has no keyframes on it. I then export at a scale of 1.0 instead of 100.0. Since switching to 1.0 export scale, I’ve had far fewer problems.
Can’t guarantee it’s the problem, but you might want to try scaling up in Blender and applying scale then exporting at 1.0. Generally, I find it’s a good idea to unparent the mesh from the armature, scale both the mesh and the armature by the same amount, apply the scale to both, and then re-parent.
Hope that helps.