To reproduce:
1. Open attached project "LightmapBug.zip"
2. Open "Test" scene.
3. In Lighting Settings set Lightmapper to "Enlighten" and Generate Lighting.
4. No shadows created.
5. In Lighting Settings set Lightmapper to "Progressive (Preview)" and Generate Lighting.
6. Shadows are created, even though gameObject "Cube" has Cast Shadows set to Off.

Reproduce from scratch:
1. Create new scene.
2. Create Directional Light.
3. Create 2 cubes, so that 1 of them would cast a shadow on the other one.
4. Change Directional Light Mode to "Baked".
5. Select created cubes and set "Cast Shadow" to off, and make them Static.
6. In Lighting Settings, change Lightmapper to "Progressive (Preview)".
7. Generate Lighting.

Actual result: Objects with "Cast Shadows" set to Off are casting shadows.
Expected result: Shadows are not casted, if object's "Cast Shadows" parameter is set to Off.

Reproducible: 5.6.0b6, 5.6.0f3, 2017.1.0b1

Note: Progressive Lightmapper added in 5.6.0b6