For SAP, down payments are not taxable.  

The down-payments module does not have the "freight" field; therefore, it does not calculate taxes.  

The only way, within the initial payment module, is to select, only for these documents, the tax mode "line item", so if you want 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´s important to clarify this, only in the down payments module you must configure this tax mode "line item". In the rest of the modules for the other documents, you can continue with the original tax mode chosen.