To reproduce on Editor:
* Have Editor Debug built (mine was Windows version) 5.2.0a3
* Open Scene 2
* Play
* Wait a bit
* "AwakeFromLoadThreaded has not been called 'ChildWithScript' (MonoBehaviour). Figure out where the object gets created and call AwakeFromLoadThreaded correctly." appears attaching screenshot

Below steps are for Windows Store Apps

To reproduce:
1. Open attached project. It contains two scenes. One scene has a signleton object that sets DontDestroyOnLoad on itself. The object also has a child
2. Build a Universal app
3. Open the generated solution with Visual Studio and deploy in a debug configuration
4. Notice that after the scenes change from green back to blue (scene1 into scene0) an error is thrown in the console:
"AwakeFromLoadThreaded has not been called 'ChildWithScript' (MonoBehaviour). Figure out where the object gets created and call AwakeFromLoadThreaded correctly."

If you remove the singleton "DestroyImmediate(gameObject);" line of code - the error is no longer thrown.

Only reproducible when deploying through visual studio, build & run does not throw the errors.