Why does .loadlevel() result in deleted game object?

So i made timer that when it reaches 0 it loads a new scene. the script for the scene change is attached to an empty gameobject called Game Manager and isn’t destroyed on load. the problem is: when the new scene loads any gameobjects other than Game Manager is labeled as “deleted gameobject”. The objects remain in the scene but cant be selected, and don’t run any scripts. Heres the script that attached to the Game Manger:
using UnityEngine;
using System.Collections;

public class gameManager : MonoBehaviour {
	public static int currentScore;
	public static int highScore;
	public static int currentLevel = 0;
	public static int unlockedLevel;

	public GUISkin Skin;
	public Rect timerRect;

	public float startTime;
	private string currentTime;

	void Update(){
		startTime -= Time.deltaTime;
		currentTime = string.Format ("{0:0.0}", startTime);
		if (startTime <= 0) {
			startTime = 0;
			Application.LoadLevel (3);

	void Start (){
		DontDestroyOnLoad (gameObject);

public static void completeLevel (){
		if (currentLevel < 2) {
			currentLevel += 1;
			Application.LoadLevel (currentLevel);
		} else {
			print ("You Win!");

	void OnGUI() {
		GUI.Label (timerRect, currentTime);

here’s the first scene (with Game Manger circled):

And here the second scene. BTW there’s only one object in the scene which is the camera:

Please help I’ve been stuck on this for a while.

Ah right, thanks for clarifying.

A couple of things strike me…

First, you don’t seem to be resetting the value of startTime at any point. Won’t this mean that once the timer runs out, the GameManager will think it’s running out all the time (so it’ll keep on loading level 3)?

Are you sure that 3 is the index of the level you want to be loading? How do you know that it has actually loaded the level you’re intending?

I hope this is your answer for your question. When unity loads a new scene,all the gameobjects in the previous scene will be deleted, unless the gameobject has a script with “DontDestroyOnLoad(gameobject)” in it