Prueba sacando la inicializacion de las variables hit1 y hit2 del Update().
var PRayo1 : GameObject;
var DRayo1 : float;
var PRayo2 : GameObject;
var DRayo2 : float;
var hit1 : RaycastHit;
var hit2 : RaycastHit;
function Update () {
Debug.DrawLine(PRayo1.transform.position, hit1.point, Color.red);
Debug.DrawLine(PRayo2.transform.position, hit2.point, Color.blue);
if(Physics.Raycast(PRayo1.transform.position, -Vector3.up, hit1, DRayo1)){
print("Rayo1");
}
if(Physics.Raycast(PRayo2.transform.position, Vector3.up, hit2, DRayo2)){
print("Rayo2");
}
}