For SAP, down payments are not taxable.  

The down-payments module does not work with the "freight" tax mode, nor with the "external tax" tax mode, only with the "line item" tax.  

The only way, within the initial payment module, is to use, only for these documents, the tax mode "line item", so if you need to calculate the tax in a down payment, you can add it as an additional line in the document the code "avatax" and in this way, it will calculate the tax on these documents. It will be shown like this

For this, if you are not using the "line item" tax mode, you should configure it as shown below

Then, re-select the original tax mode that you´ve been using, and be sure to check the two options shown below.