Question Instantiated Object not following Physics Matrix.

Not sure what I'm doing wrong here. Forgive me for I'm a bit of newbie. I have a prefab that when I drag and drop it into the scene the collision matrix works fine. I have currently set it on a layer labeled TransparentFX and have (for testing purposes) removed all collision with every layer.

However, when I instantiate the object, it ignores the physics matrix and instead collides with every single layer, regardless of what is checked or unchecked. I have checked the layers on the instantiated object, and although they are children of a skinned mesh renderer, their layer and tag is still the correct one.

Here's the code.

Code (CSharp):

1. Vector3 position = AVG(edge.vertices);
2.                 Vector3 normal = AVG(edge.normals).normalized;
3.                 var rotation = Quaternion.FromToRotation(_prefabDirection, normal);
4.  
5.                 var m = skinnedRenderer.sharedMesh.bindposes[maxIndex];
6.                 position = m.MultiplyPoint3x4(position);
7.  
8.                 blood = Instantiate(_bloodPrefab, bone);
9.                 blood.transform.localPosition = position;
10.                 blood.transform.localRotation = rotation;

And here's the physics matrix proof.