How to reproduce:
1. Open the attached "SurfaceShaderStrangeness" project
2. Open "asdf" scene, double click on "Shader_Broken" in Project window to open it
3. Comment #ifdef and #endif lines on 26th and 28th line
4. Notice that the "Plane" has a red color

Expected result: "Plane" should have had a red color, before commenting #ifdef line
Actual result: "Plane" didn't have a red color, until commenting #ifdef and #endif lines in Input struct

Regression introduced in 5.6.0b2
Reproducible with 2017.1.0a3, 5.6.0f2, 5.6.0f1
Not reproducible with 5.6.0b1, 5.5.2p3, 5.4.5f1

Note: Alternatively to a 3rd step on how to reproduce the issue, you can just change "Plane" material shader from Custom/Broken to Custom/NoIfDef (this shader simple removes #ifdef from Input struct)

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Fixed in 2017.3.0a4