Having canonical problems like that is a bit of a different thing from whitelists, isn't it?
Ted is it? I am not so sure.
maybe it's related to consistent internal linking.
The whole site diplayes in ip, non and www. If this were to happen to a site of mine today it would be nuked. There has to be something that prevents this site being effected. I have watched this site go through all the Google updates nothing has ever effected it. I have for along time suspected a whitelist. I might add the links were added 3-4 years ago so if it was a past problem it didn't work then either.