Hi,
The partner for orders do not use these fields for sales fees but the order_partner_xxx fields of the hikashop_order table.
If you go in the Affiliate->Clicks menu, do you see the click of your user B ?
If you look in the cookies of the browser of user B, do you see an affiliate cookie for your website ?
If yes, it means that the system detected the user B as being an affiliate of the other user. Otherwise, edit the user A via the HikaShop customers listing and make sure that the affiliate program is activated for him.