Colliders Stop working when using Game manager

So I had what essentially amounted to a breakout type game that was working well until I started trying to build my game manager. Once I removed the prefabs from the scene and started instantiating them with the game manager, the colliders stopped working between the paddle (ie seesaw) and the ball (ie caveman in my script.

Can anybody tell me what step I've missed in the game manager or something I should be checking on my prefabs?

Here is my game manager script.

using UnityEngine; using System.Collections; using System.Collections.Generic; using UnityEngine.UI;

public class GM : MonoBehaviour {

 public int lives = 3;
 public int birds = 20;
 public float resetDelay = 2f;
 public Text livesText;
 public GameObject RightBorder;
 public GameObject LeftBorder;
 public GameObject Ground;
 public GameObject gameOver;
 public GameObject youWon;
 public GameObject bluebirdsPrefab;
 public GameObject redbirdsPrefab;
 public GameObject greenbirdsPrefab;
 public GameObject SeeSaw;
 public GameObject HumanBoom;
 public GameObject BlueBirdBoom;
 public GameObject GreenBirdBoom;
 public GameObject RedBirdBoom;
 public static GM instance = null;
 public GameObject pjbase;
 private GameObject cloneSeeSaw;
 private GameObject BlueBird;
 private GameObject GreenBird;
 private GameObject RedBird;
 private GameObject Caveman;
 private GameObject ground;
 private GameObject leftB;
 private GameObject rightB;
 // Use this for initialization
 void Awake()
 {
     if (instance == null)
         instance = this;
     else if (instance != this)
         Destroy(gameObject);

     Setup();

 }

 public void Setup()
 {
     cloneSeeSaw = Instantiate(SeeSaw, SeeSaw.transform.position, Quaternion.identity) as GameObject;
     BlueBird = Instantiate(bluebirdsPrefab, transform.position, Quaternion.identity) as GameObject;
     RedBird = Instantiate(redbirdsPrefab, transform.position, Quaternion.identity) as GameObject;
     GreenBird = Instantiate(greenbirdsPrefab, transform.position, Quaternion.identity) as GameObject;
     Caveman = Instantiate(pjbase, pjbase.transform.position, Quaternion.identity) as GameObject;
     rightB = Instantiate(RightBorder, RightBorder.transform.position, Quaternion.identity) as GameObject;
     leftB = Instantiate(LeftBorder, LeftBorder.transform.position, Quaternion.identity) as GameObject;
     ground = Instantiate(Ground, Ground.transform.position, Quaternion.identity) as GameObject;
 }

 void CheckGameOver()
 {
     if (birds < 1)
     {
         youWon.SetActive(true);
         Time.timeScale = .25f;
         Invoke("Reset", resetDelay);
     }

     if (lives < 1)
     {
         gameOver.SetActive(true);
         Time.timeScale = .25f;
         Invoke("Reset", resetDelay);
     }

 }

 void Reset()
 {
     Time.timeScale = 1f;
     Application.LoadLevel(Application.loadedLevel);
 }

 public void LoseLife()
 {
     lives--;
     livesText.text = "Lives: " + lives;
     Instantiate(HumanBoom, cloneSeeSaw.transform.position, Quaternion.identity);
     Destroy(cloneSeeSaw);
     Invoke("SetupSeeSaw", resetDelay);
     CheckGameOver();
 }

 void SetupSeeSaw()
 {
     cloneSeeSaw = Instantiate(SeeSaw, transform.position, Quaternion.identity) as GameObject;
 }

// public void DestroyBirds() // { // birds--; // CheckGameOver(); // } }