One of the many things you might look into to help explain the problem is Proxy Hacking. Check out a post by Dan Thies called: Google Proxy Hacking: How A Third Party Can Remove Your Site From Google SERPs .
The gist of this is that there is strong evidence suggesting some unethical competitors, hackers and blackhat SEOs have been linking to URLs on proxy servers so Google indexes a copy of your page. Especially for domains with low trust-rank, this has the potential to get your site dropped from the indexed or pushed down the SERPS as duplicate content.
Every webmaster, web developer and SEO should read the article above. It is likely to happen much more often now that the tactic has been made so public. For what it’s worth, I think it was the right thing to do.
If you are operating a proxy server you can prevent it from being used as a nefarious tool by adding a rule to your robots.txt file that prevents all search engine spiders from indexing proxied content through your server:
User-agent: *
Disallow: /proxy/
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