I would robots.txt your redirect scripts and also consider there is a thought that although G maybe not able to tell what your jump script is they may look for patterns that suggest redirect scripts or aff links are being used.
For example a page that only has ten links to a file called click.php might flag your page as a serp page or as a feed site even though click.php is a file on your own site.
I think Google know that its hard for them to always identify where feed and aff links have been hidden so instead they look for patterns in design, patterns in linking all that sort of stuff.
That said if you read the rest of this thread you will see that my own lead gen site got whipped, no aff links or feeds in sight there. Google are really just encouraging people to adopt throwaway domains as its the only quick way to get back in.
Don't take it personally - it doesn't mean your site sucks at all, any serious marketeer knows that quality score is a big scam and the public tide of opinion will turn against google in the end, albeit slowly (show me an empire that lasts for ever.)
The other ppcs know they need to treat their advertisers and affiliates with more respect to gain market share, unfortunately g has so much cash and resources they now think showing respect is entirely optional and that hopefully will be their undoing.
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