it's imposible to tell what the problem is without first doing some debugging.
to help troubleshoot, create a new blank page and add a eCart display manager to it.
on the second step of the display manager wizard, click the plus button and select the option to show all column.
on the third step of the display manager wizard, set the Discounts, shipping, taxes, and charges to Show individually.
this will create a cart display page that gives a more complete view of the cart details.
on this page, add the following code just before the </body> tag to show the session contents:
<pre><?php var_dump($_SESSION); ?></pre>
send a link to your site and steps to reproduce the problem, a link to the new cart display page for troubleshooting, and a copy of the cart object file in the WA_eCart folder in a zip archive.