This option involves the module always adding the cheapest amount between the configured national shipping services in the “SHIPPING” tab and making it free on eBay, then deducting that amount from the cost of the remaining configured shipping services (both national and international).

Therefore, make sure that the current configuration never includes a service with FREE SHIPPING (0.00), otherwise the module will not modify the eBay listing in any way because it will add zero to the product cost and subtract zero from the other shipping services offered on eBay, resulting in no visible changes.