controller.Move not working correctly

Hi, I am having a problem with moving a gameobject with a collider attached. I am using the collider.Move function: when I press "space" to jump, my character quits moving forward shortly after leaving the ground. If I increase my jump height, the character will move for part of the jump, but not all of it. The character always moves on the downward part of the jump and the first part of the upward part of the jump. Soon after leaving the ground, all movement on the x axis stops. I have done some logging, and the velocity.x remains a constant 1.5 this whole time. My character consists of a gameobject with a character controller, script, and animation attached. It also has a armature system attached as a child. I have completely disabled all animation, with no better results. I will attach my script as a reference.

 #pragma strict
 
 var playerMoveSpeed : float = 1.5;
 var jumpVelocity : float = 6.2;
 var gravity : float = 20.0;
 var moveDirection : int = 0;                        //reference for changing the direction the knight is facing
 var controller : CharacterController;
 
 
 private var velocity : Vector3;
 
 function Start ()
 {
     controller = GetComponent (CharacterController);
 }
 
 function Update ()
 {
     if (velocity.x > 0)                                //sets move direction
     {
         moveDirection = 0;
     }
     if (velocity.x < 0)                             //left
     {
         moveDirection = 1;
     }
     if (moveDirection == 0)                          //changes knight direction based on move direction, right
     
     {
         transform.localScale.z = 1;
         transform.eulerAngles = Vector3(0,180,0);
     }
     if (moveDirection == 1)                         //left
     {
         transform.localScale.z = -1;
         transform.eulerAngles = Vector3(0,0,0);
     }
     
     velocity.x = -1.5; //Input.GetAxis("Horizontal") * playerMoveSpeed;  I hardcoded the movement in to make sure I don't have an input issue.
     
     if (controller.isGrounded)                        //allows jumping while on ground.
     {
         if (Input.GetButtonDown ("Jump"))
         {
             velocity.y = jumpVelocity;
         }        
     }
     velocity.y -= gravity * Time.deltaTime;            //apply gravity
     controller.Move(velocity * Time.deltaTime);        //actually does the moving on character controller
     
     print (velocity.x);
     print (velocity.y);
     print (Time.deltaTime);
 }