FindObjectOfType broken in 5.3

Unity Engine
1

Since Unity introduced new SceneManager, using static var for singleton manager objects doesnt work.
In my set up, as suggested by the Unity team itself in the manual (and common sense) i have a
manager stack in a separate scene that is never unloaded.

Previously there was no problem as singletons were accessed with FindObjectOfType
now however it doesnt work anymore if the call happens from other scene.
I do hope its me whos doing something wrong and not bug in unity. It is actually weird because i do
recall it working just a few days ago with other project, but now it refuses.
If i put the manager object in the same scene as the requesting object, the method works and instance is received.

Here is thread on answers with exact same issue, please tell me what im doing wrong.
http://answers.unity3d.com/questions/1115848/gameobjectfindobjectoftype-not-working-in-unity-53.html#answer-form

2

i found this
taking into account you advise to have managers in one scene, i just wonder how you thought people should do that.
This is not acceptable.

3

The problem : cross links are broken
the real problem: manager scene initialization happens AFTER other scene

Solution: drag manager scene on top of game scene, making it initialize before game.
This is acceptable, and logical, cheers.