Rigidbody movement conflict?

It is because immediately after adding force you are hard setting the velocity of the rigidbody, overriding the force added. You need to maintain the Y-velocity.

Edit : Sorry for the late reply. I didn't have time to give an example, but tbkn has given an example of what I was describing. And it seems like my comment was converted to answer, so I have stripped down one of my player code projects to give an example for future readers. Even though stripped down it is quite long, the main part is in the function ApplyMovement() where (again as tbkn demonstrated) the rigidbody velocity Y is maintained in the calculated velocity before applying to the rigidbody.

 calcVel.y += myRigidbody.velocity.y;

Hopefully you'll see some interesting stuff in my below code :

 //------------------------------//
 //  RigidbodyMovement.js        //
 //  Written by Alucard Jay      //
 //  4/8/2014                    //
 //------------------------------//
 
 #pragma strict
 
 
 public var moveSpeed : float = 7.0;
 public var jumpVelocity : float = 120.0;
 public var airMovementModifier : float = 0.1;
 public var velocityLerpTime : float = 0.05;
 public var maxSlopeAngle : float = 60.0;
 public var inputDeadZone : float = 0.05;
 
 public var isAlive : boolean = false;
 
 private var myTransform : Transform;
 private var myRigidbody : Rigidbody;
 
 private var desiredVelocity : Vector3 = Vector3.zero;
 private var inputVector : Vector3 = Vector3.zero;
 private var isGrounded : boolean = false;
 private var isJumping : boolean = false;
 
 
 
 //  Persistant Functions
 //  ------------------------------------------------------------------------------------------------
 
 
 function Awake() 
 {
     Initialize();
 }
 
 
 function Start() 
 {
     myTransform = transform;
     myRigidbody = transform.rigidbody;
 }
 
 
 function Update() 
 {
     if ( !isAlive )
     {
         return;
     }
     
     // -- MOVEMENT -- 
     GetPlayerInput();
     ApplyMovement();
 }
 
 
 function FixedUpdate() 
 {
     if ( isAlive )
     {
         myRigidbody.velocity = desiredVelocity;
     }
 }
 
 
 //  Other Functions
 //  ------------------------------------------------------------------------------------------------
 
 
 function Initialize() 
 {
     isAlive = true;
 }
 
 
 // PLAYER INPUT
 //  ------------------------------------------------------------------------------------------------
 
 function GetPlayerInput() 
 {
     // reset inputVector
     inputVector = Vector3.zero;
     
     // get movement inputs
     var horz : float = Input.GetAxis("Horizontal");
     var vert : float = Input.GetAxis("Vertical");
     
     // get player Vertical input
     if ( vert < -inputDeadZone || vert > inputDeadZone )
     {
         inputVector += Vector3( 0, 0, vert );
     }
     
     
     // get player Horizontal input
     if ( horz < -inputDeadZone || horz > inputDeadZone )
     {
         inputVector += Vector3( horz, 0, 0 );
     }
     
     // get player Jump input
     if ( Input.GetKeyDown(KeyCode.Space) )
     {
         isJumping = true;
     }
 }
 
 
 // APPLY MOVEMENT
 //  ------------------------------------------------------------------------------------------------
 
 function ApplyMovement() 
 {
     // calculate the direction for the force to be applied
     var calcVel : Vector3 = myTransform.TransformDirection( inputVector.normalized ) * moveSpeed;
     
     // check if jumping, add Jump velocity, 
     // else maintain current Y velocity
     if ( isJumping )
     {
         calcVel.y = jumpVelocity;
         
         isJumping = false;
     }
     else
     {
         // maintain current Y velocity
         //calcVel.y = myRigidbody.velocity.y;
         // add velocity.y instead of hard setting it
         calcVel.y += myRigidbody.velocity.y;
     }
     
     // calculate desired velocity
     if ( !isGrounded )
     {
         // calculate desired velocity
         calcVel *= airMovementModifier; // restrict movement while airborne
         calcVel += myRigidbody.velocity * ( 1.0 - airMovementModifier ); // maintain velocity while in the air
         desiredVelocity = Vector3.Lerp( myRigidbody.velocity, calcVel, velocityLerpTime );
     }
     else
     {
         // calculate desired velocity
         desiredVelocity = Vector3.Lerp( myRigidbody.velocity, calcVel, velocityLerpTime );
     }
 }
 
 
 //  Is Grounded Collision Events
 //  ------------------------------------------------------------------------------------------------
 
 
 var currSlopeAngle : float = 0.0; // Debugging slope angle
 
 
 function OnCollisionEnter( collision : Collision )
 {
     for ( var contact : ContactPoint in collision.contacts )
     {
         if ( Vector3.Angle( contact.normal, Vector3.up ) < maxSlopeAngle )
         {
             isGrounded = true;
         }
         
         
         // ----
         
         currSlopeAngle = Vector3.Angle( contact.normal, Vector3.up );
         
         // ----
     }
 }
 
 
 function OnCollisionStay( collision : Collision )
 {
     for ( var contact : ContactPoint in collision.contacts )
     {
         if ( Vector3.Angle( contact.normal, Vector3.up ) < maxSlopeAngle )
         {
             isGrounded = true;
         }
         
         
         // ----
         
         // Debugging slope angle
         // character is climbing slopes
         
         currSlopeAngle = Vector3.Angle( contact.normal, Vector3.up );
         
         // ----
     }
 }
 
 
 function OnCollisionExit()
 {
     isGrounded = false;
 }