In this sample project I have created a simple sprite with a shader. The shader gets a color and modulates the sprite with that color.
Now I have set all sprites of gbot to z-layer 5. And the sprite with the shader to z-layer 1.
Now when the sprite with the shader comes into the screen gbot gets modulated by that color to.
Just run to the right until you reach the node.
Here is the sample project
https://www.dropbox.com/s/up9oj2wnkux9stn/shader_bug.zip?dl=0