What also happens, is that a customer will purchase the first product from a different affiliate. Then in between the first sale, and the upsell will visit your website, thereby overwriting the first affiliate's cookie with yours. Then when the upsell is made, you get the payment, instead of the original affiliate. It happens quite often actually. The person makes the initial purchase, then goes out and does more research before buying the upsell.
I have seen this happen to me. This is what probably happens: -The customer buys the product from another affiliate link. -After the purchase, he surfs around for more info on the product regarding the upgrade -The customer clicks another affiliate link, in this case, your link -You get the commission for the upsell