Reproduction steps:

1. Open "ShaderAssetBundleTest.zip" project
2. Open "TestScene" Scene
3. Enter Play mode
4. Look at the two Game Objects (Left - Custom Shader, Right - Standard Shader)
5. Exit Play Mode
6. Open "Loader" Scene
7. Enter Play Mode
8. Look at the two Game Objects

Expected Result: The Left Game Object should look like in the "TestScene" scene
Actual Result: The Left Game Object doesn't look as expected

Fixed with: "Scriptable Build Pipeline" package

Reproduced with: 2018.3.0a9, 2018.2.4f1, 2018.1.9f1, 2017.4.9f1, 2017.3.2f1

Note:
Need to rebuild bundles through versions
"Window" -> "AssetBundle Browser" -> "Build" -> "Build"