Reproduction steps:
1. Open attached project "RebuildInstanceBug"
2. Open scene "bug"
3. Observe the Game window
4. Enter Play mode
--- You should notice that both cubes have become much lighter (see attached screenshots)

Code that causes this issue:
void Start ()
{
Renderer rend = GetComponent<Renderer> ();
ProceduralMaterial mat = (ProceduralMaterial)rend.material;
mat.RebuildTexturesImmediately ();
}

Regression introduced in: 5.2.1p1 (9d7f6c38e90b)