How to reproduce:

1. Create a new project.
2. Create a Plane and a Cube and set them as Static. Move the cube above the Plane so you can see a shadow from the Cube.
3. Set the Directional Light to Mixed Baking mode.
4. Press Window -> Lighting and on the Scene tab next to the Build button uncheck Auto checkbox. Press Build and save Scene.
5. Create a Sphere and also position it above the plane so you can see the shadow.
6. Go to Edit -> Project Settings -> Player and on the Other Settings switch the Rendering Path to Deferred.
7. Notice how the Sphere shadow will start flickering but the Cube shadow will be fine.

Reproducible: 5.4.0b20, 5.4.0b21, 5.3.5f1, 5.2.4f1.