Steps to reproduce:

1. Open attached project
2. Open scene "ShaderPropertyBug"
3. Run scene
4. Notice that cube is red
5. Select "Cube" in hierarchy
6. Expand its instance of material
7. Notice that when material gets expanded, emission is applied

Expected result: Emissive property is applied as soon as the scene is played

Workaround: Since emission is applied using Renderer.material.SetColor("_EmissionColor", Color.white ); add Renderer.material.EnableKeyword("_EMISSION");