On the Webmaster Central blog, Google has made some clarifications on how the site command works. By adding excluding the www in front of the domain you are doing a site command search for, you can include subdomains in the results.
A search for www.site.com returns URLs that begin with www and a search for site.com returns URLs for all subdomains. (So, site:google.com returns URLs such as www.google.com, checkout.google.com, and finance.google.com).
Unfortunately, if your site either purposely or through bad planning has non www pages indexed such as http://domain.com/page.html, then those pages will not be returned in the www search and you cannot get an accurate reading of your main domains index. You will either need to fix the issue through a 301 htaccess rule or through the Google Webmaster Central backend.