Player keeps going through the floor when crouching.

Hi all, I got an next problem with JS script: Why my player keeps going through the floor if I crouch? Can't understand what I'm doing wrong or how to prevent this from happening, floor has mesh collider and my player is the basic FPS Controller with character controller and rigidbody.

Here's the movement.js script which includes the code for crouching.

 var mainCam : GameObject;
 var animObject : GameObject;
 var fallAnimGO : GameObject;
 var moveSpeed : int = 2;
 var crouchSpeed : int = 1;
 var runSpeed : int = 5;
 var jumpSpeed : int = 10;
 var gravity : int = 20;
 var maxEnergy : float = 10;
 var energyRegenRate : float = 1;
 var Smooth : float = 5;
 
 var grounded : boolean = false;
 var running : boolean = false;
 
 var energy : float;
 private var originalSpeed : int;
 private var hitCeiling : boolean = false;
 public var moveDirection = Vector3.zero;
 private var controller : CharacterController;
 controller = GetComponent(CharacterController);
 
 private var IntialPosition : Vector3;
 private var InitialHeight : float;
 private var CrouchingHeight : float;
 private var InitialCenter : Vector3;
 private var CrouchingCenter : Vector3;
 private var defCamPos : float = 0;
 private var bobSpeed : float;
 private var bobAmount : float;
 private var timer = 0.0;
 private var camPos : float;
 private var crouching = false;
 
 function Start()
 {
     originalSpeed = moveSpeed;
     energy = maxEnergy;
     defCamPos = mainCam.transform.localPosition.y;
     camPos = defCamPos;
     InitialHeight = controller.height;
     CrouchingHeight = InitialHeight - .5f;
     InitialCenter = controller.center;
     CrouchingCenter = InitialCenter + Vector3.down * 0.1f;
     isCrouching = false;
 }
 
 function Awake()
 {
     animObject.animation.wrapMode = WrapMode.Loop;
 }
 
 function Update()
 {
     if(controller.isGrounded)
     {
         moveDirection = new Vector3(Input.GetAxis("Horizontal"), 0, Input.GetAxis("Vertical"));
         moveDirection = transform.TransformDirection(moveDirection);
         moveDirection *= moveSpeed;
         if(Input.GetKeyDown(KeyCode.Space))
         {
             Jump();
         }
         if(controller.velocity.magnitude > (moveSpeed - 1) && controller.velocity.magnitude < (runSpeed - 1))
         {
             animObject.animation.CrossFade("Walk");
             bobSpeed = 0.25;
             bobAmount = 0.005;
         }
         else if(controller.velocity.magnitude > (runSpeed - 1))
         {
             animObject.animation.CrossFade("Run");
             bobSpeed = 0.29;
             bobAmount = 0.01;
         }
         else
         {
             animObject.animation.CrossFade("Idle");
             bobSpeed = 0;
             bobAmount = 0;
         }
         if(Input.GetKey(KeyCode.LeftShift) && (Input.GetAxis("Horizontal") || Input.GetAxis("Vertical")))
         {
         
             if(energy > 0)
             {
                 if(!crouching)
                 {
                     Run();
                 }
                 else
                 {
                     moveSpeed = crouchSpeed;
 
                 }
             }
             else
             {
                 running = false;
                 if(!crouching)
                 {
                     moveSpeed = originalSpeed;
                 }
                 else
                 {
                     moveSpeed = crouchSpeed;
                 }
             }
         }
         else
         {
             running = false;
             if(energy < maxEnergy)
             {
                 energy += energyRegenRate * Time.deltaTime;
             }
             if(!crouching)
             {
                 moveSpeed = originalSpeed;
             }
             else
             {
                 moveSpeed = crouchSpeed;
             }
         }
         
         var camHeight : Vector3 = new Vector3(mainCam.transform.localPosition.x, camPos, mainCam.transform.localPosition.z);
         var smoothHeight  = Vector3.Lerp(mainCam.transform.localPosition, camHeight, Time.deltaTime * Smooth);
         mainCam.transform.localPosition = smoothHeight;
         
         if(Input.GetKeyDown("c"))
         {
             if(!crouching)
             {
                 controller.height = CrouchingHeight;
                 controller.center = CrouchingCenter;
                 camPos = defCamPos - .5f;
                 crouching = true;
             }
             else
             {
                 controller.height = InitialHeight;
                 controller.center = InitialCenter;
                 camPos = defCamPos;
                 crouching = false;
             }
         }
         waveslice = 0.0; 
         horizontal = Input.GetAxis("Horizontal"); 
         vertical = Input.GetAxis("Vertical"); 
         if(Mathf.Abs(horizontal) == 0 && Mathf.Abs(vertical) == 0) { 
               timer = 0.0; 
         } 
         else
         { 
                waveslice = Mathf.Sin(timer); 
                timer = timer + bobSpeed; 
                if(timer > Mathf.PI * 2)
                { 
                   timer = timer - (Mathf.PI * 2); 
                } 
         } 
         if(waveslice != 0)
         { 
                translateChange = waveslice * bobAmount; 
                totalAxes = Mathf.Abs(horizontal) + Mathf.Abs(vertical); 
                totalAxes = Mathf.Clamp (totalAxes, 0.0, 1.0); 
                translateChange = totalAxes * translateChange; 
                mainCam.transform.localPosition.y = smoothHeight.y + translateChange; 
         } 
         else
         { 
            mainCam.transform.localPosition.y = smoothHeight.y; 
         } 
     }
     else
     {
         animObject.animation.CrossFade("Idle");
         bobSpeed = 0;
         bobAmount = 0;
     }
     moveDirection.y -= gravity * Time.deltaTime;
     if(hitCeiling)
     {
         moveDirection.y -= gravity * Time.deltaTime;
     }
     var flags = controller.Move(moveDirection * Time.deltaTime);
     hitCeiling = ((flags & CollisionFlags.CollidedAbove) != 0);
     if(energy > maxEnergy)
     {
         energy = maxEnergy;
     }
 }
 
 function Run()
 {
     moveSpeed = runSpeed;
     energy -= energyRegenRate * Time.deltaTime;
     running = true;
 }
 
 function Jump()
 {
     moveDirection.y = jumpSpeed;
     fallAnimGO.animation.CrossFadeQueued("Jump", 0.1, QueueMode.PlayNow);
 }
 
 function OnControllerColliderHit(Hit : ControllerColliderHit)
 {
     if(!controller.isGrounded && controller.velocity.y < -6)
     {
         fallAnimGO.animation.CrossFadeQueued("Fall", 0.3, QueueMode.PlayNow);
     }
 }