It sounds like the shipping charge is just not being triggered. If there were a problem during the quote request you should be redirected to the shipping failure page. It is almost as if you have the following value set in the globals file:
$WAGLOBAL_Shipping_Enabled = false;
This needs to be true for shipping to work, but I'm sure you are already doing that based on what you have stated here.
On your confirm pages you can get the full request and full response from the shipping quote request by putting this php code in the places on the page where you would like to see this info:
<?php echo $_SESSION["WA_Store_Cart_UPS_FullRequest"]; ?>
<?php echo $_SESSION["WA_Store_Cart_UPS_FullResponse"]; ?>
Please post back with whatever you discover.