Reproduction steps:
1. Open the attached project (lighting problem repro.zip);
2. Open the scene "lighting issues.unity";
3. In the game view, observe lighting difference between the sphere with standard shader and the instanced surface shader;
4. Open the ModelShader.shader script;
5. Comment the 85 line;
6. In the game view, observe that the spheres are lit identically.

Expected results: the custom instanced surface shader will work as the standard.
Actual results: objects are lit differently;

Reproduced on: 5.3.6p8, 5.4.2p4, 5.5.0f2, 5.6.0a3.

Note:
85 line: In this line is evaluated the Surface shader's occlusion:
o.Occlusion = tex2D(_OcclusionMap, IN.uv_MainTex) * _OcclusionStrength;