Shader input arrays not getting set Unity 5.4

Steps to Reproduce
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1.Download the small user reproduction project
2.Open the project in 5.3, open the 'test' scene and run in the editor.
3.Note that there are no problems, you will see 16 white squares.
4.Open the same project in the latest 5.4
5.Open the 'test' scene and run in the editor.

Result
When running in 5.4.x you will note that a single black square is visible.

Expected Result:
Sixteen white squares should be visible.

See the 5.3.x Vs 5.4.x comparison screenshot in the comments below.

Tested in
5.3.5f1 (960ebf59018a) - working
5.4.0b18 (5744ebf94ac5) - broken
5.4.0b11 (323b0238353b) - broken