Steps to reproduce:

1) Download attached project 'Preloading.zip' and open in Unity.
Note: Make sure that Graphics API is set to Direct3D9.
2) Open scene 'Main'.
3) Open the Profiler and view the CPU section.
4) Press Play.
5) In Game tab, click on "Step 1 - Material.SetPass (Preload)" button.
Notice in the Proflier that shows huge spike in Material.SetPassUncached (this is expected).
6) Now click on Click "Step 2 - Instantiate".
Notice in the Proflier that shows huge spike in Material.SetPassUncached (this is NOT expected).

Note: It doesn't happens every time after those steps, If you wasn't able to reproduce it from the first time, try again.
I was able to reproduce with OpenGLCore once.
Wasn't able to reproduce with DX11

Reproduced with: 5.3.5p8, 5.3.6f1, 5.4.0f1.
Not reproduced with: 5.5.0a3