Hubpages , Blogger or Wordpress are good examples in which bad subdomains DO NOT affect rankings of good subdomains despite linking between subdomains or between subdomain and main domain .
I would say a bad subdomain should not affect main domain rankings if the main domain has good/relevant content .
Maybe you should remove affiliate pages and see what happens next .
In my case noindex and 404 thin/duplicate content did not helped , many good pages still ranked badly . Only after i moved to subdomain some pages i saw improvements only for those pages . Main domain still pandalized
But only 20 days since the move , bad things can still happen