GG expands on his suggestion about URL schemes and 301 redirecting other URLs tot he preferred one. He doesn't say whether there were any changes in this area during the recent update, but one might speculate that this could be the case, based on the detailed attention he pays the topic here...
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Hey, about the redirect--Google tries to find the canonical version of a page, but technically in html I think that all of
can be different pages (not sure about the trailing slash, but I think so). So Google tries to figure out the best page to call canonical, but it never hurts to give a spider extra help. If you want www.domain.com to be the canonical, you can make domain.com and www.domain.com/index.html be a permanent redirect to www.domain.com. I remember a long time ago (months?) someone had moved to a new domain, and olddomain.com did a 301 to newdomain.com, then newdomain.com did a 301 to newdomain.com/index.html, and so on. Instead of creating a long chain like that, I'd pick one page you want to be canonical (I'd recommend www.domain.com) and make aliases that you don't want be a 301 to that canonical page. As steveb mentioned we normally get it right, esp. compared to the infrastructure changes of a few months ago, but it never hurts to give a spider extra help.
Let's see. Bek, nobody has an "in" with Google, although you wouldn't believe the number of folks who try to claim that. :) I checked out the site you mentioned, but many boxes were checked (Hidden text or links, Deceptive redirects, Doorway pages, and Duplicate site or pages), and I didn't see that at first glance. So it's possible that someone checked it out and didn't see what you reported. I saw some words in the noframes section, but that's it. Could you say in a spamreport what exactly was wrong with the site?