Reproduction steps:
1) Open user's attached project
2) Import 2 scenes into hierarchy (SceneA and SceneB)
3) Make SceneB appear under SceneA in hierarchy
4) Make SceneB - "Active Scene"
5) Enter playmode

Expected result:
SceneB should remain "Active Scene"

Actual result:
"Active Scene" switches to SceneA

Note:
If in playmode you will mark "Active Scene" any other Scene (regardless was it done with Script or right mouse click > Set Active Scene) exiting playmode will make "Active Scene" SceneA (Scene which is on top of hierarchy view).

Regression happened from 5.3