Repro steps:
1. Open "LightmapBugReport" project
2. Load "demo1" and "demo2" scenes
3. Open Lighting Window
4. Under the Lightmaps tab make sure that Auto (next to build) is disabled
5. Press Build
6. Observe that two lightmaps appear completely the same
Note: If you build lightmaps with Auto enabled everything works alright. Scroll down for user's picture.
Also sometimes only one lightmap gets baked and you get scene distortion.

Actual behavior: Duplicate lightmaps appear under Lightmaps tab
Expected: Different color lightmaps should appear under Lightmaps tab

Reproduced on: 5.4.0f3, 5.5.0a6
Could not test on previous versions because of errors.