Hi there.
NOINDEX !== no crawling. and surely it doesn't equal NOFOLLOW. what you probably should be looking at is canonical links.
My understanding is (and i can be completely wrong) that when you get hit by Panda for duplicate content and then try to recover, Google checks your website for the same duplicate content - it's still crawlable, all the links are still "followable", it's still scraped content, you aren't telling crawlers that you took it from somewhere else (by canonicalizing), it's just not displayed in SERPs. And yes, 80% of content being noindex probably doesn't help either.
So, I think that what you need to do is either remove that duplicate content whatsoever, or use canonical links to originals or (bad idea, but would work) block all those links in robots.txt (at least this way those pages will become uncrawlable whatsoever). All this still is unreputable techniques though, kinda like polishing the dirt.
Hope this makes sense.
