To reproduce:
1. Open attached StencilBugs (u5.2.2f1) or StencilBugs (u5.6.0b10) project
10. Load the scene 'Stencil_MPB_Bug'
11. Notice you can't see the sphere through either sides, it is acting as the stencil Ref Value is set to 0
12. Select Portal_2 gameObject and try changing the Stencil Ref Value to 1 or 2
13. Notice it still does not appear in either side
14. Press Portal_Diffuse_ID_2 and notice that it is set to 0 ( if you change it to 1 or 2 sphere appears on one or both sides of cube)

Actual result: Changing the Stencil Reference Value via inspector does not affect Gameobjects
Expected result: Changing the Stencil Reference Value in Inspector changes Gameobject material value.

Reproduced on: 5.2.2f1; 5.5.2p3; 5.6.0b10; 2017.1.0a3
Not reproduced on: 4.7.1

Note: gifs added.