Steps to reproduce:
1. Open attached project
2. Load Scene "B"
3. Make sure Scene "A" is unticked in File>Build Settings
4. Enter Play mode
5. Check console - "0 Assets/B.unity" is logged
6. Build project (for Windows)
7. Check console - "1 Assets/B.unity" is logged

Expected result: the index of Scene B is always logged as 0 if it is the first active scene in the list
Actual result: the index of Scene B is logged as 1 after building a project

Reproducible with: 5.6.0f3, 2017.2.0f3, 2018.1.0a6