Adam Lasnik, Google's new poster boy, wrote a thread at WebmasterWorld named Google's site: query returns bad results - now being fixed. In that thread he links to a Inside Google Sitemaps blog entry the describes the site command bug in more detail.
They explained they found a "few" bugs with the site command which would show less or supplemental results for your particular search. The two bugs they listed are;
site: queries where you type in a trailing slash (such as site:www.example.com/)
site: queries for a domain with punctuation (such as site: www.example-site.com)
They said, they hope to fix it in the next few days. Until then, they recommend using the site:www.example.com syntax.