Steps to reproduce:
1. Open the attached project (New Unity Project 13.zip)
2. Switch to Windows Store
3. Build and Run the Menu3d scene
4. Hit close
5. Open Scenes in Build in Build settings
6. Build and Run the qq scene
7. Observe the previous scene were built

Expected result: Unity should build the scene in Scenes in Build
Actual result: Unity builds the previous scene

Reproduced with: 2017.1.0f1
Not reproduced with: 2017.1.0b10, 2017.2.0b1