Steps to reproduce:
1. Download and open attached project
2. Open scene "AssetLoader"
3. Run Assets-->AssetBundles-->Build AssetBundles
4. Select Assets-->AssetBundles-->Simulation mode
5. Hit play
6. See blue and red squares
7. Stop playing
8. Unselect Assets-->AssetBundles-->Simulation mode
9. Select Assets-->AssetBundles-->Local AssetBundle Server
10. Hit play
Video in edit

Expected result: 1 blue and 1 red square
Actual result: 2 red squares

Reproduced on: 5.2.3f1, 5.3.6f1, 5.4.1p3, 5.4.2f1, 5.5.0a1
Note: 5.5.0a1+, 5.3- shaders gets lost entirely(squares end up as pink during runtime)

Note: User notes that changing shader_feature to multi_compile in ShaderWithVarients fixes this problem, but makes too many possible shader configurations in his regular project. I was unable to replicate this behaviour