Lobby manager problem - Player Object running Start() and Awake() before gamescene .

I had my game working fine with the networkmanager so decided to now move to using the lobby asset. With network manager I create my players in this method:

Code (CSharp):

1.     public override void OnServerAddPlayer(NetworkConnection conn, short playerControllerId)
2.     {
3.         if (conn.connectionId == 0)
4.         {
5.             Vector3 pos = new Vector3(-8.5f, 0, 0);
6.             Quaternion rot = Quaternion.Euler(new Vector3(0, 0, -90));
7.             GameObject player = (GameObject)Instantiate(playerPrefab, pos, rot);
8.             player.name = "Player0";
9.             ShipScript shipScript = player.GetComponent<ShipScript>();
10.             shipScript.Player = conn.connectionId;
11.             ShipScript existingPlayer = GameManagerScript.Players.Find(x => x.Player == conn.connectionId);
12.             if (existingPlayer == null)
13.                 GameManagerScript.Players.Add(shipScript);
14.             NetworkServer.AddPlayerForConnection(conn, player, playerControllerId);          
15.         }
16.         else
17.         {
18.             Vector3 pos = new Vector3(8.5f, 0, 0);
19.             Quaternion rot = Quaternion.Euler(new Vector3(0, 0, 90));
20.             GameObject player = (GameObject)Instantiate(playerPrefab, pos, rot);
21.             player.name = "Player1";
22.             ShipScript shipScript = player.GetComponent<ShipScript>();
23.             shipScript.Player = conn.connectionId;
24.             ShipScript existingPlayer = GameManagerScript.Players.Find(x => x.Player == conn.connectionId);
25.             if (existingPlayer == null)
26.                 GameManagerScript.Players.Add(shipScript);
27.             NetworkServer.AddPlayerForConnection(conn, player, playerControllerId);
28.             //GameObject.Find("GameManager").GetComponent<GameManagerScript>().Active = true;
29.         }          
30.     }

Lobby manager doesn't appear to have an OnServerAddPlayer method so I've used this instead:

Code (CSharp):

1.         public override GameObject OnLobbyServerCreateGamePlayer(NetworkConnection conn, short playerControllerId)
2.         {
3.          
4.             if (conn.connectionId == 0)
5.             {
6.                 Vector3 pos = new Vector3(-8.5f, 0, 0);
7.                 Quaternion rot = Quaternion.Euler(new Vector3(0, 0, -90));
8.                 GameObject player = (GameObject)Instantiate(playerPrefab, pos, rot);
9.                 player.name = "Player0";
10.                 ShipScript shipScript = player.GetComponent<ShipScript>();
11.                 shipScript.Player = conn.connectionId;
12.                 ShipScript existingPlayer = GameManagerScript.Players.Find(x => x.Player == conn.connectionId);
13.                 if (existingPlayer == null)
14.                     GameManagerScript.Players.Add(shipScript);
15.                 //NetworkServer.AddPlayerForConnection(conn, player, playerControllerId);
16.             return player;
17.             }
18.             else
19.             {
20.                 Vector3 pos = new Vector3(8.5f, 0, 0);
21.                 Quaternion rot = Quaternion.Euler(new Vector3(0, 0, 90));
22.                 GameObject player = (GameObject)Instantiate(playerPrefab, pos, rot);
23.                 player.name = "Player1";
24.                 ShipScript shipScript = player.GetComponent<ShipScript>();
25.                 shipScript.Player = conn.connectionId;
26.                 ShipScript existingPlayer = GameManagerScript.Players.Find(x => x.Player == conn.connectionId);
27.                 if (existingPlayer == null)
28.                     GameManagerScript.Players.Add(shipScript);
29.                 //NetworkServer.AddPlayerForConnection(conn, player, playerControllerId);
30.                 //GameObject.Find("GameManager").GetComponent<GameManagerScript>().Active = true;
31.             return player;
32.             }
33.         }

First seems to work fine. The problem is that I have code in my ShipScript in Awake() and/or Start() that requires components in the gamescene. In the old version, this was fine and it would find the objects but with the lobby it's not working and i get null reference on the find. Presumably, the player objects are created just before the scene is loaded?

I imagine it's pretty important for gameobjects in the gamescene to be able to run their Start() within that actual scene. Am I doing something wrong?