How to prevent discounting on non-inventory billable items

The vertex software is supposed to manage TAX based on State/Product/City/County/Customer and calculates TAX on invoice line items. In some states Freight is TAXED and Freight should be appeared as Line Item. We have defined freight as a non shippable item and will enter it as order line on sales order, but had issues with the invoice, where the freight is being discounted. We don't want to calculate discount on non-shippable items like freight/service tax/warranty etc. Currently non-shippable lines are part of fullfillment set with the product that is being shipped to avoid separate invoice just for freight. How to