For example, if a customer makes a purchase of 100$ with 5$ shipping fee and program commission is 10%, the commission will be calculated only based on 100$. Thus, affiliate commission is 10% of 100$ which is 10$. If you want to include shipping fee, please do not enable the button, in that case, affiliate commission is 10% of 105$ (100$ + 5$) which is 10.5$.