This is the correct spot. Are you using discounts? The line in question is:
id="amount_<?php echo $eleventh_step_store_Index+1; ?>" value="<?php echo WA_eCart_FormatNumber($eleventh_step_store->DisplayInfo("Price") - (($eleventh_step_store->DisplayInfo("Price")/$eleventh_step_store->TotalColumn("TotalPrice")) * $eleventh_step_store->GetDiscounts()), false, 2) ?>"
You can update it to something like:
id="amount_<?php echo $eleventh_step_store_Index+1; ?>" value="<?php echo WA_eCart_FormatNumber($eleventh_step_store->DisplayInfo("Price") + $eleventh_step_store->DisplayInfo("YourShippingColumnName"), false, 2) ?>"