To reproduce:
1. Open attached project;
2. Open "scene" scene;
3. Open Lighting window and clear baked data;
4. Select one of the game objects (f.e. sofa_for_script);
5. In the Top menu, press VRnet > Generate UV-map of selected objects;
6. Generate Lighting (Lighting > Scene > Generate Lighting).

Expected result: Baked lights with autogenerated lightmap UVs and created with Unwrapping.GenerateSecondaryUVSet() are exactly the same.
Actual result: Baked lights with autogenerated lightmap UVs and created with Unwrapping.GenerateSecondaryUVSet() are different.

Reproduced on versions: 5.5.5f1, 5.6.3p4, 2017.1.1f1, 2017.1.1p3, 2017.2.0f2, 2017.3.0b2.