Character wont jump on moving object

I have two sets of platforms: one set is moving downward and the others are moving upward. The character will not jump on the downward platforms, but will on the upward ones. Im using CharacterController.isGrounded method of collision to be able to jump. My guess is that its not registering that connection when the platform is essentially falling, but the character is clearly standing on it because it will animate the walk while moving back and forth as if it is registering the grounding. Any ideas?

Thanks!

  void Update() 
         {
             //Assign static variable
             stopControls1 = stopControls;
 
             //Move Player
             PlayerRun();
         }
     
         //Player control
         void PlayerRun()
         {
             if(!stopControls)
             {
                 //Check if is on the ground
                 if(charController.isGrounded)
                 {    
                     //If grounded, set to false
                     walkJumpOn = false;
                     runJumpOn = false;
                     crouchJumpOn = false;                
 
                     if(!isCrouched)
                     {
                         if (!freeFall) 
                         {
                             //Set key movement
                             moveDirection = new Vector3 (Input.GetAxis ("LeftAndRight"), 0);
                             charController.Move (moveDirection * Time.deltaTime);
                         }
 
                         //Rotate 
                         if (moveDirection != Vector2.zero)
                         {
                             Quaternion newRotation = Quaternion.LookRotation(moveDirection);
                             
                             thisTransform.transform.rotation = Quaternion.Slerp(thisTransform.transform.rotation, 
                                 newRotation, Time.deltaTime * 20);
                         }
                         
                         //If is moving
                         if(moveDirection.magnitude > 0.05f)
                         {
                             //walk 
                             if(!Input.GetKey(KeyCode.M))
                             {
                                 maxSpeed = 6;
 
                                 moveDirection *= walkSpeed;
                                 thisTransform.GetComponent<Animation>().CrossFade("Run");    
                             }
                             //run
                             else
                             {
                                 maxSpeed = 10;
 
                                 moveDirection *= runSpeed;
                                 thisTransform.GetComponent<Animation>().CrossFade("Sprint");
                             }
 
 
                         //idle
                         else 
                         {
                             thisTransform.GetComponent<Animation>().CrossFade("Idle");
                         }
                     }
 
                     //JUMP COMMANDS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                     //Idle jump height
                     if(Input.GetButtonDown("Jump") && (!Input.GetKey(KeyCode.M) || Input.GetKey (KeyCode.M) 
                         && moveDirection.x == 0) && Input.GetAxis("Crouch") >= 0)
                     {
                         AudioControl.JumpSound();
 
                         CreateDust();
 
                         moveDirection.y = walkJump;
                         moveDirection.x = walkSpeed;
                         walkJumpOn = true;
                     }
                     
                     //Sprinting jump height
                     if(Input.GetButtonDown("Jump") && Input.GetKey(KeyCode.M) && moveDirection.x != 0)
                     {
                         AudioControl.JumpSound();
 
                         CreateDust();
 
                         moveDirection.y = runJump;
                         runJumpOn = true;
                     }
                     
                     //Walking jump height
                     if(Input.GetButtonDown("Jump") && moveDirection.x == 0 && Input.GetKey(KeyCode.S))
                     {
                         AudioControl.JumpSound();
 
                         CreateDust();
 
                         moveDirection.y = walkJump;
                         crouchJumpOn = true;
                     }
 }
 
 //If not on the ground...
                 if(!charController.isGrounded)
                 {
                     //Assign inputs
                     moveDirection.x = Input.GetAxis("LeftAndRight");
                     
                     //If jump key is let go, fall to the ground
                     if(Input.GetButtonUp("Jump"))
                     {
                         moveDirection.x = 0;
                         moveDirection.y = moveDirection.y - fallSpeed;    
                     }
 //Create gravity
                 moveDirection.y -= gravity * Time.deltaTime;
                 
                 //Check for jump input
                 charController.Move(moveDirection * Time.deltaTime);    
             }     
         }