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The pages concerned (index pages on 2 sites) both have some content generated by javascript. One was an experiment with client-side rather than server-side includes, the other is a script-generated affiliate link. Of course it could be a coincidence, but neither page breaks any rules and its the only thing they have in common.
I know Google doesn't generally read javascript, but is it possible that it can now seek out the document.write command? - I ask because I have seen threads here where people suggest that document.write is a good way to hide content from search engines. Perhaps Google has caught on.
Anyone have any ideas?