I'm using the Affiliates plugin with Pro Sites and the Stripe gateway.
I created an affiliate link for testing purposes and, in a fresh, incognito browser window, visited the affiliate link and signed up.
The click was tracked and the signup was tracked.
In the same window, while logged in to the new account, I made a payment to upgrade to a paid site.
The payment never showed up in the affiliate area, both as the affiliate and the network admin. For "Paid Members" it still shows 0.
Obviously the cookie was created and tracked up to the point of signing up, but the affiliate was never credited for the purchase.