Steps to reproduce:

1) Download attached project 'ShaderVariantCollection.zip' and open in Unity
2) In the Project window, go to Assets >> ABs folder and delete all AssetBundles
3) Select 'ShaderAndMaterial' folder and in the menu items(top) select Assets >> TestAssetBundle
4) Select ABs folder and click on Select Folder button
5) In the Hierarchy window, select LoadAll gameObject and change absolute paths to Assets >> ABs filder
6) Press Play
Observe white cubes on the screen

Expected result: Loaded cubes as an assetBundle with ShaderVariantCollection should be in red color (check attached image 'expectedColor.png')
Actual result: Cubes are white because their loses variants (check attached image 'lostVariants.png')

Reproduced with:
2017.1.0a1, 2017.1.1f1, 2017.2.0b10, 2017.3.0a7

Not reproduced with:
5.6.3p2

Regression since:
2017.1.0a1

Note: Video of reproduction is attached
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Fixed in: 2018.1.0a1, 2017.4.0f1, 2017.3.0b6, 2017.2.0p1