When Shipping Label Integration is not enabled and a Real Time Rate Shipping Item is being used yet the shipping cost is always calculating as zero. First check to make sure the item has weight assigned to it and is not listed as a Free Shipping Item on the Shipping Item record.
1. Navigate to Setup> Company> Company Information
2. Check the UPS and FedEx 3rd Party Billing Account Number fields to determine if these are filled out.
**Without Shipping Label Integration enabled the 3rd party billing account number can have an affect on the shipping cost without the preferences available to change them.
3. Delete both the account number and billing Zip code and Shipping Cost will calculate correctly.
4. Click Save.