You should be getting taxation if setup correctly. Check how the freight is taxed, by clicking the right arrow icon -> to the right of the freight amount. The in our case we attach the tax to the debtor so depending upon the country to which the order is shipped, we get different tax rates. In example below UK VAT at 20% is applied from the Ship to Tax Schedule ID in the Debtor Detail Entry window of the sales order. I don't know your setup but perhaps the screen shots will help point you in the correct places.
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