Procedual Collider is not working correctly - Until reset in editor C#

I'm in the process of creating a Procedural game and I'm having an issue with my characters collider. I'm using this code to generate the collider:

 GameObject i = Instantiate (playerObj,playerSpawn,Quaternion.identity) as GameObject;
 i.name = "Player";
 i.tag = "Player";
 i.AddComponent<CapsuleCollider>();
 i.AddComponent<Rigidbody>();
 i.AddComponent<PlayerController>();
 i.GetComponent<CapsuleCollider>().center = new Vector3(0,0.5f,0);
 i.GetComponent<CapsuleCollider>().radius = 0.25f;

The code is only run once. This should in my mind give something like this

But instead I get this:

The character can still move in the same manner (including jumping) and doesn't seem to be stuck into the ground. The values of the Collider are correct in the inspector however if I edit the value during runtime via the inspector the Collider fixes itself, even with the same values entered. Does anyone know why this is and how I might fix it?