I have a multisite with both prosites and affiliates.
The affiliate program seems to be tracking clicks but not recording sign-ups on the Affiliate Reports and the Referred By column is empty on the Network Admin Sites report.
I've read through your community and saw that this had been a problem in the past but supposedly had been corrected a couple of years ago.
I have a 30 day free trial on prosites - should that matter? It seems that you would still need the referrer info. I have 60 days set for the cookie.
I know for a fact that CKing sent out an email with affiliate link http://promo.usingessentialoils.com?ref=cking-47 and that maureenfedail followed that link and registered for a site. They were on different computers. Neither the Network Admin Sites page or Affiliate Reports shows the referral.