FP Character won't move in New Scene till I load it a second time!

Any help with this would be truly appreciated as I am thoroughly stumped as to why this is not working right.

So in my game you can bring up a map, and when you click on certain locations it loads a new level for the first person player to explore. (This is all done by UI's )

I've tried both having the character not be destroyed during the loading process and just having a new FP character ready in the new scene - right now I have a new FP character - but either way, when first entering a new scene the character refuses to move. Yet when you bring up the map again and either choose your current location again or another location it works. Basically it only ever works on the second click.

That is weird right!?

I'm not really sure what is causing the problem but I thought I'd attach the FPS script and the loading one for now, if anyone thinks it could be something else, just say and I'll find the script.

This is the FPS script:

 public float speed = 6.0F;

 public float gravity = 20.0F;
 private Vector3 moveDirection = Vector3.zero;
 void Update()
 {
     CharacterController controller = GetComponent<CharacterController>();
     if (controller.isGrounded)
     {
         moveDirection = new Vector3(Input.GetAxis("Horizontal"), 0, Input.GetAxis("Vertical"));
         moveDirection = transform.TransformDirection(moveDirection);
         moveDirection *= speed;


     }
     moveDirection.y -= gravity * Time.deltaTime;
     controller.Move(moveDirection * Time.deltaTime);
 }

And this is the load scene script:

 public GameObject loadingImage;

 public void LoadScene(int level)
 {
     loadingImage.SetActive(true);
     Application.LoadLevel(level);
 }

}

I was determined to figure this out by myself, but I just have no idea where to even start! Thank you so much for having a look.