Steps to reproduce:

1) Download attached project " BugTest.zip " and open in Unity.
2) Open scene "FlickeringBug".
3) In Hierarchy tab, select Sphere.
4) In Scene view, rotate view /move Sphere from 0.0.0 position.
Note : Everything works as it should be. (see attached gif "alright.gif").
Move sphere back to 0.0.0 position.
5) In inspector, set Material2 shader to Custom/PlanetLights.
Note : If you rotate view while Sphere in 0.0.0, it works as expected.
But if you move it somewhere, you will see flickering of 2nd material.(see attached gif "wrong.gif").

Reproduced with: 5.4.0b21, 5.4.0b24.

Not reproduced with: 5.2.4f1, 5.3.5p6, 5.4.0b20.