I don't have answers for you... just adding my voice to the same topic.
I never knew until a year or so after the event about Google deciding that links out to the affiliate site had to be rel="nofollow" (there are probably many thousands of site owners who don't belong to forums who still don't know that). So that is something that you can do yourself and the sooner the better if not already done.
There are two affiliate merchants I was no longer willing to partner with so I removed all my links to their product pages. But GWT says there are hundreds of merchant links still in existence to my site like:
I have asked the merchant to delete/404/no follow these links, which they have not done and instead they are redirecting the 404 event to their home page.
The fact that GWT is still seeing these as IBL's a year or more after leaving the merchant, and now having been hit by Penguin (unnatural links), I am wondering if these links are the problem.... and if so, then Google is apparently not disregarding all affiliate links.