2D Sorting Layer don't worn with new material

I was just as confused as you are, I'll tell you what worked for me. I was using Unlit/ToonLitSprite, and all I had to do was change the setting "render queue" to transparent.

Hi @THretroGames,

Excellent question!

That is correct, and this is by design. The sorting layer actually modifies some material properties to tell the GPU what order to render things. If the new material doesn't have the same properties, this won't work. If you are willing to modify the material yourself, you can add control over the sorting order.

Check out this thread, discussing what you're seeing: http://forum.unity3d.com/threads/drawing-order-of-meshes-and-sprites.212006/