I've never played the affiliate game from either direction before, but I've taken on a client who does, and now I'm confused.
When I search on ATW using link.all:example.com I see in the SERPs some pages that contain links from affiliates, but the anchor tags on those affilate pages all point to another domain, such as CJ's http://www.qksrv.net/
[affiliate code here]
So how does ATW know that the anchor tag eventually goes to my client site? I like it, but I'm just a bit boggled. I'm also wondering if ATW is following other, non-affiliate redirects in the same way.
Tedster, I don't have any good input for you. Currently I don't see any redirect urls listed in backlinks, none. OTOH I'm pretty sure ATW can follow redirect urls and properly recognize the final destination. To make things even more complicated the backlink functions at ATW show some rather irregular behaviour in general these days.