I have a model that was rigged and animated in maya but as soon as i bring the fbx of that model in unity its mesh geometry is deforming ( vertices are not at the same position as they can be seen in maya ).I have tested the fbx in 3ds max and blender also and everything seems to be fine , looks like the problem is only in unity.
I might had have something similar(ish) with my model/joints. Just to take a guess here, you didnt resize the joints did you? You just rotate the joints and then bake in Maye to Unity? Or …? I could be of no use here but worth a shot to try and help