Q:

Unity: Weird scene transition bug after adding a "Persistent-Scene" with a GameManager

I made a pretty basic 2D game to learn. I have 2 Scenes, and switching between them worked great. I used empty gameObjects as Start/Exit point of the Scene, so that the game would know to put player on point X after exiting through point X (for example exit outside house if I walk out the door).
Then I added a "Scene0", to use for persistent general scripts like GameManager, Sounds, Music, etc. With just one object called "Controller" that I DontDestroyOnLoad().
After adding this Scene and then just switching Scenes right away to my MainScene, all of a sudden the game starts acting really strange; 
the first time I move from my MainScene (Scene1), to my secondary Scene (Scene2), it works fine, but then when I leave Scene2 to go back to Scene1, the player spawns in the middle of nowhere.
And this ONLY happens if I launch the game from my Persistent Scene.
I have no idea what is wrong, I don't add anything that interferes with my scene transitions, all I've added so far is playerHealth, for testing.
Scripts attached to my (persistent) Controller:
DDOL:
public class DDOL : MonoBehaviour {

    // Use this for initialization
    void Awake () {
        DontDestroyOnLoad (gameObject);
    }

}

GameManager:
public class GameManager : MonoBehaviour {

    public static GameManager manager;

    public int playerMaxHealth;
    public int playerCurrentHealth;

    void Awake(){
        if (manager == null) {
            manager = this;
        } else if (manager != this) {
            Destroy (gameObject);
        }
    }

    // Use this for initialization
    void Start () {
        SceneManager.LoadScene("test_scene");
    }

    // Update is called once per frame
    void Update () {

    }
}

Scripts attached to my StartPoint:
PlayerStartPoint:
public class PlayerStartPoint : MonoBehaviour {

    private PlayerController thePlayer;
    private CameraController theCamera;

    public Vector2 startDir;

    public string pointName;

    // Use this for initialization
    void Start () {
        thePlayer = FindObjectOfType<PlayerController> ();

        if (thePlayer.startPoint == pointName) {
            thePlayer.transform.position = transform.position;
            thePlayer.lastMove = startDir;

            theCamera = FindObjectOfType<CameraController> ();
            theCamera.transform.position = new Vector3(transform.position.x, transform.position.y, theCamera.transform.position.z);
        }
    }
}

And finally ExitPoint:
LoadNewArea:
public class LoadNewArea : MonoBehaviour {

    public string levelToLoad;
    public string exitPoint;
    private PlayerController thePlayer;

    // Use this for initialization
    void Start () {
        thePlayer = FindObjectOfType<PlayerController> ();
    }

    void OnTriggerEnter2D(Collider2D other){
        if (other.gameObject.name == "Player") 
        {
            SceneManager.LoadScene(levelToLoad);
            thePlayer.startPoint = exitPoint;
        }
    }
}

EDIT: 
After moving all my DDOL gameObject to the Pre-Scene, it worked. So, I can assume the fault is inside Player or Cameras Start() functions since when they start in Scene1 they get called every time I enter the Scene (only DDOL). 
I tried adjusting their Start()functions like follows:
Original camera:
void Start () {
        Debug.Log("Starting camera");
        if (!cameraExists) {
            cameraExists = true;
            DontDestroyOnLoad (gameObject);}
           else{
        Destroy (gameObject);
        }
    }

Changed Camera:
void Start () {
            DontDestroyOnLoad (gameObject);
        }

The exact same changes was made in Player.
Obviously this doesnt work because it creates a new Camera/Player every time I enter Scene1 (btw why does it not try to create them when I enter Scene2?, is it because they start in Scene1?). HOWEVER, the new player/camera do start at the correct position, and if I zoom out I can see the old player/camera at that same wrong position as before. So something weird happens when their Start() is called a second time it seems.

A:

You've now mentioned that you had code something like this,
void Start () {
        Debug.Log("Starting camera");
        if (!cameraExists) {
            cameraExists = true;
            DontDestroyOnLoad (gameObject);}
           else{
        Destroy (gameObject);
        }
    }

Note that this is unfortunately just "utterly incorrect", heh  :)
The issues you mention in the question (preload scenes etc) are just totally unrelated to the problem here.

In Unity if you have a character C that persists between scenes a, b, c as you load those scenes, you must kick-off C in it's own (perhaps otherwise empty) scene, you can not use "a" as a matter of convenience to kick off C.
The pattern is, in each of a, b, c just have a line of code like p = FindObjectOfType<Player>(); which runs when the scene loads, and position C as you wish.

Now, regarding your specific puzzle about the unusual behavior you are seeing.
I understand that you want to know why you are observing what you do.
It is a combination of confusion over the following issues:  1 - difference between Awake and Start,  2 - confusion over script execution order {but see below1}  3 - confusion about Destroy versus DestroyImmediate  4 - Not using Debug.Log enough, and not using gameObject.name in there (it's a common in Unity to be wildly confused about which object is talking in Debug.Log)  5 - where you mention you see the other object "off to the side", it's common to drastically confuse which one is which in such situations  6 - confusion between the computer programming concept of "instantiation" (ie, of a class or object) and "instantiating" (confusingly, it's the same word - utterly unrelated) game objects in nity.
If you fiddle around with all those issues, you'll discover an explanation for the behavior you're seeing!
But it doesn't amount to much; in Unity in the "C .. a b c" example you have to create C separately beforehand.
1 {aside, never fiddle with the script execution ordering system in Unity in an effort to solve problems; it's only there for R&D purposes; however it could in fact help you investigate the behavior at hand in this problem, if you are particularly keen to fully understand why you're seeing what you're apparently seeing}

A:

Use the debugger. Have breakpoints at the relevant spots, like PlayerStartPoint.Start() and LoadNewArea.OnTriggerEnter2D() and check that they are executed

At the right time
The right number of times
With the expected values

This should make you see where things get out of hand.
If you use Visual Studio, install https://marketplace.visualstudio.com/items?itemName=SebastienLebreton.VisualStudio2015ToolsforUnity to be able to debug Unity from within Visual Studio.
If you are not using Visual Studio, you probably should.

