In my studies, search engines often tend not to like web articles with affiliate links in them. It is my observation that leans towards stating that affiliate links may reduce the rank a websites page gets on the internet.

Web spiders can scan for affiliate links by looking for common keywords such as "affiliate?" or "affil/id" or "id=" or even a link that seems to be completely random i.e. "http://arksaio.com/KalAkaiuLska9skI2l," because those are also used for affiliate links.

So it seems bad practice (except for easy organization) to have anything referencing the meaning "affiliate" in the link for affiliates. Those affiliate program providers may be reducing the ranks to pages that are selling their products. So, to remedy this, those who make affiliate programs, just use a "r", a "z", or something else to reference affiliates if you need the organization.

Also, some web masters may have also noticed this trend, and may not use your affiliate program due to the fact that it may lower their websites pages ranks (i.e. websites popularity).