To reproduce:
1. Open attached project
2. Open "test" scene
3. Hit play and notice that mesh is drawn in gray color
4. Select "test" game object in hierarchy and disable "Use Property Block"
5. Now hit play and notice that shape is drawn in red color

Expected: In both situations mesh color is red because the only difference is how compute buffer is set (directly or not).
Actual: When color is set through MeterialPropertyBlock with ComputeBuffer it doesn't effect Graphics.DrawMeshInstancedIndirect.

Reproduced with : 5.6.0a3, 5.6.0b10, 5.6.0f3, 5.6.1p1, 2017.1.0b6, 2017.2.0a1

Was not able to test on earlier versions of Unity because of not available features, which were introduced in 5.6 version.

Workaround: Setting compute buffer to a material with Material.SetBuffer (directly).

Fixed in 2017.2.0a2
Backported to: 5.6.2p3, 2017.1.0f3