To reproduce:
1. Open attached project in Unity 5.5
2. Open main.unity
3. Press play to run script "HaloEx.cs" which will set the shader to "Resources/Internal-Halo.shader" ( This is the same as the Internal-Halo shader from standard shaders, but is hard coded to return fixed4(1,0,0,1); as the final colour.

Actual: HaloEx.cs has no effect. Also notice in "Built-In shader settings" in Graphics settings, a new shader is added as "Motion Vectors"
Expected: Light Halo Shader should be set to Resources/Internal-Halo.shader

Reproducible: 5.5.0p1, 5.6.0a6
Not reproducible with 5.4.3p3