This will have to do with the setup of the External Supplier Invoice Parameters, the Tax Recalculation field setting. If you wish to use the amounts from the load file, set this field to None. 

This is from help:

Use this field to specify how the tax amount included in the external file should be recalculated when loading external supplier invoices. The selected parameter is only considered if no tax code is included in the external file. The possible values are as follows:

• Tax Amount and Non-Deductible Tax Amount - If this is selected, tax code(s) is fetched from the company/supplier and tax amount on the tax line(s) is recalculated by applying the relevant taxes to the invoice amount in the external file. Further, tax amount on the invoice line also get updated once tax is recalculated. Tax and non-deductible tax is calculated separately by taking deductible percentage of each tax code into consideration.

• Tax Amount Only - If this is selected, tax code(s) is fetched from the company/supplier and tax amount on the tax line(s) is recalculated by applying the relevant taxes to the invoice amount in the external file. All tax codes are considered as 100% deductible irrespective of the deductible percentage entered on the tax codes.

• Non-Deductible Tax Amount Only - If this is selected, tax code(s) fetched from the company/supplier is not 100% deductible, then the tax amount on the tax line is recalculated. If the connected tax code is 100% deductible, then the tax amount is not recalculated and hence the tax amount included in the text file is treated as the tax amount.

• None - If this is selected, neither the tax amount nor the non-deductible tax amount is recalculated even if the tax code is not included in the external invoice file.

Note: If multiple tax exist, parameters ‘Non-Deductible Tax Amount Only’ and ‘Tax Amount and Non-Deductible Tax Amount’ will produce same results.

Our suppliers provide us with a Net Amount, Tax Amount and Gross Amount. There is no tax rate on the invoices for bring in.  The problem is then IFS is assigning it a 0 tax code and recalculating incorrectly.  Not sure how the 0 is getting applied when that is not on the external invoice.

I see, this is used to load invoices directly from the supplier and there will be no tax code there. There is a window where we can define the tax code to apply for the external supplier invoices based on the tax percentage on the invoice. This can be per supplier or applied to all, using * and % parameters as in my example. 

You can define the default rule applying to everything, and then by exception add a line per supplier/country if it’s different.