i dont have enough information to answer your question.
from the code you posted i can see that you are using the eCartCheckoutForm_Ship_Type variable to set a global variable, the using that as a trigger for the shipping rate lookup:
<?php
if($WAGLOBAL_Shipping == 1) {
?>
<?php
//WA eCart UPS Shipping Include
require_once("WA_eCart/WA_eCart_UPS_PHP.php");
?>
<?php
if ($_SERVER["REQUEST_METHOD"] == "POST") {
If they select 1 it triggers the UPS shipping lookup.
once triggered, it stores the quote in a session, that session is used to trigger the UPS shipping rule in the cart.
if they change it to something else, the UPS quote session still exists
I have no idea how you have configured the other options though.