It is an interesting theory Voodooman, I too have heard the rumblings that Affiliate based sites are treated harsher than other sites. Our site doesn’t use Javascript re-directs, but we do employ a similar sort of re-directing using ASP code. We did that originally to keep track of click throughs to casino sites. I’m not the technical one, but it seems that Google may not follow this code as well, though I’m not really sure how to check that. I can go to Google sitemaps and they give me a list of error pages when Google tries to follow certain links. So far it has been because of sites that have gone down that we were linking too (fastpoker.com for instance). So maybe this means that Google is following our links.
In any case, you may want to look at our site and see if that helps out your theory or not.