Reproduction steps:
1. Open the attached project "SubstanceTextureRebuildRepro.zip";
2. Open the TestScene;
3. Enter a play mode.

Expected results: all three cubes had the same texture applied to them and are set to be different colors. After rebuilding textures, colors should remain the same.
Actual results: all cubes are painted in the one color after rebuilding.

Reproduced on: 5.6.0a1. 2017.1.2p3, 2017.2.0p2, 2017.3.0b10, 2018.1.0a5.
Not reproduced: 5.5.5p1 and lower.
Regression has started in: 5.6.0a1.

Note: while Play mode is starting, you can see for a moment how cubes are with different colors and then they all turn to one color.