Disabling scaling in unity animations?

I have imported an fbx model into unity, the model was exported from Blender along with all of the animations, materials, etc. Now I have written a function where I can scale different sections of the armature, this works fine when no animations are playing, however if an animation is playing then the scaling will not work. Now I made sure in blender that my animations involved no scaling, just position and rotation movement, so I am stumped for a reason why I cannot edit the scale of the armature, while an animation is playing?