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Not the same thing. I'm talking about a site with pages containing lots of hidden stuffing. The question was whether just naughty pages are penalised or the whole domain.
Since the original post I've done a search for the whole domain name, as in "www.domainname.com". Google responds with a "not found in index" message so I'm interpreting that as a penalty on the domain.
If that's the case, the question becomes "then why are some lower level pages still showing?" I'm guessing here but:
1) perhaps Google has only only "processed" some of the site and the remaining pages will vanish in later updates.
2) maybe the remaining pages are not considered naughty and get to stay in the index.
Time will tell I guess.