Steps to reproduce:

1. Download and open attached project (link in edit notes)
2. Open 'EditorScene'
3. Rebuild lightmaps with current settings
4. Build and run the game with 'EditorScene' only
5. Build and run the game with both 'MenuScene' and 'EditorScene' (you'll need to click start to load 'EditorScene' then)
6. Compare the lighting of two builds (lighting where the 'EditorScene' is loaded directly is way brighter as if lightmap wasn't loaded correctly. See screenshots)

Note: lighting in editor is always the same regardless of whether 'EditorScene' is loaded directly or through 'MenuScene' using LoadLevel (it looks similar to the lighting in built game when the 'EditorScene' is loaded with Application.LoadLevel)

Reproduced with: 5.3.0f2, 5.3.0f3, 5.4.0a5