The following code does not have any problems jumping using isGrounded. It also clamps vertical velocity to the maximum free fall velocity of 120 mph (53 meters/second).

using System.Collections;
using System.Collections.Generic;
using UnityEngine;
public class PlayerMovements : MonoBehaviour
{
 public CharacterController player;
 public float WalkSpeed = 8f, TurnSpeed = 2f, JumpForce = 4f;
 public float VerticalVelocity = 0f;
 public Vector3 Movements = new Vector3 (0, 0, 0);
 void Awake()
 {
   player = GetComponent<CharacterController> ();
 }
 void Update ()
 {
   if (!player.isGrounded)
  {
    VerticalVelocity += Physics.gravity.y * Time.deltaTime;
    VerticalVelocity = Mathf.Clamp (VerticalVelocity, -53f, JumpForce);
    Movements.y = VerticalVelocity;
   } else {
    VerticalVelocity = 0f;
    Movements.x = Input.GetAxis ("Horizontal") * WalkSpeed;
    Movements.z = Input.GetAxis ("Vertical") * WalkSpeed;
    if(Input.GetButtonDown ("Jump"))
    {
     VerticalVelocity += JumpForce;
     VerticalVelocity = Mathf.Clamp (VerticalVelocity, -53f, JumpForce);
     Movements.y = VerticalVelocity;
    }
   }
   player.Move (Movements * Time.deltaTime);
  }
}