An observation based on mentions of "low quality" in Amit Singhal's blog post at http://googlewebmastercentral.blogspot.com/2011/05/more-guid... -- you mention that you have no-indexed thin content pages, but is it possible that if Google sees that the volume of "noindex" pages is high compared to the overall volume of pages on the site, that Google still views your site as overall of "low-quality" (relative to the other sites it indexes for the same keywords)?

Rather than noindex pages, I am thinking using robots.txt to prevent access to these pages might be better -- Google can't perhaps then tell what to make of these pages you've hidden via robots.txt. Just thinking...not really an expert on this.