Vanessa Fox from Google Engineering posted at the Inside Google Sitemaps blog, that Google found a bug with the site search command. The post explains that some of the reason people are noticing indexing issues at Google, is because of this bug. The two of a "few bugs that affected the site: operator" include using the site command with a trailing slash (i.e. site:www.example.com/) or trying it on a hyphenated domain name (i.e. site:www.example-site.com). Google says they will have it fixed within a few days, but until then, use the syntax site:www.example.com. I have the forum roundup on this bug at the Search Engine Roundtable.
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