I was able to do a test of your shipping charge rule with your cart files. I created a new test page with an add to cart on it and I also added a new cart display to the page. I manually set the WA_TD_Shipping session variable to 5. When I ran my test I was able to see the transdirect $5.00 charge.
This tells me that you shipping rule is setup correctly, but there might be a problem with the session variable. When I check for where you are setting the session variable I think I can see the issue. Rite now you have the session variable set like this:
$_SESSION["WA_TD_Shipping"] = "$WA_TD_Response";
I think the problem is that you are setting it to a string like this rather than the value of the response. I think it should be like this:
$_SESSION["WA_TD_Shipping"] = $WA_TD_Response;
From the test I did I can see that if you have this session variable set, and it is greater than 0 you should be charged whatever value is held in the session variable. If it does not hold a proper value you will not see the charge.
A way that you can test this out is to print out the session variable on your confirm page like this:
<?php echo $_SESSION["WA_TD_Shipping"]; ?>