Have you found that when you applied the map the lines are ticked as taxed but the rate is 0% ? (as shown below in yellow in image on the right).
This is most likely due to this supplier having incorrect default settings. To check go to the Admin Tab> Suppliers; Edit and select the supplier. If it's 'Default Tax Code' says 'No GST', 'GST Free' or similar, then please remove it and leave this field blank.Then refresh the page & apply the map.
This field is best left blank to allow the maps to work correctly, as we will use your 2 default company tax rates you've set. Only in special circumstances would you need to select a different default tax code.
If after making these changes the problem still occurs, then please check that your company's default Tax Rates you've ticked are correct (via Admin Tab > Tax Rates; Edit)
This example below shows you the 2 standard tax rates that are typically selected;
If after making this change it still maps as 0%, then please give us a call.