Steps to reproduce:

1. Open attached project.
2. Open scene: a
3. Open scene b and c in additive (drag&drop)
4. Make active scene not the top one.
5. Save SceneSetup (use this custom window ET -> SceneManager)
6. Restore SceneSetup

Expected result: Scenes are restored as they were before saving.
Actual result: Any scenes that are above active scenes are gone after restoring

Note: They are saved correctly, as you can see them in the foldout.

Reproduced on 5.5.0b1