Material RenderQueue does not match Shader RenderQueue

Symptoms

• Objects may appear in unexpected depths
• Order in Layer is ignored i.e. in Sprite Renderer

Causes

This might have occurred for a couple of reasons:

• By using an Editor or Runtime script that intentionally overrides the Material.renderQueue of the material. This material could then be duplicated or reused in another project expecting that the RenderQueue is inherited by the Shader's RenderQueue. For example:
  

  gameObject.GetComponent<Renderer>().sharedMaterial.renderQueue = 2000;

• By using an older version of Unity (prior to 5.1.3, see More Information below), which did not reset the Material RenderQueue when a new Shader was assigned to the material.

Resolution

Reset Material RenderQueue to the Shader RenderQueue.

The following Editor script goes through all the Materials in the project and sets the Material RenderQueue to the Shader RenderQueue:

using UnityEditor;
using UnityEngine;

public class ResetMaterialsRenderQueue
{
	[MenuItem ("Assets/Reset Materials RenderQueue")]
	static void DoResetMaterialsRenderQueue()
	{
        Material[] materials = (Material[])Resources.FindObjectsOfTypeAll(typeof(Material));

	    int materialsLength = materials.Length;

	    for (int i = 0; i < materialsLength; ++i)
	    {
	        if (materials[i].shader != null)
	        {
	            materials[i].renderQueue = materials[i].shader.renderQueue;
	        }
	    }  
	}
}

More Information

Release notes for 5.1.3 - Graphics: Switching shaders in the material inspector should reset the material's RenderQueue to default.
This article applies to Unity versions 5.2+

Further Instructions

• Download the file below
• Unzip into Assets/Editor folder
• In Unity Editor, go to Assets and select Reset Materials RenderQueue