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.
In some cases, a site: search doesn’t show a full list of results even when the pages are different, and we are resolving that issue as well. Note that this is a display issue only and doesn’t in any way affect search rankings. If you see this behavior, simply click the “repeat the search with omitted results included” link to see the full list. The pages that initially don’t display continue to show up for regular queries. The display issue affects only a site: search with no associated query. In addition, this display issue is unrelated to supplemental results. Any pages in supplemental results display “Supplemental Result” beside the URL.
Google says they are working on the issue. I actually just saw a change to one domain that now says “Results 1 – 2 of about 350″ instead of 260. Only 20,410 pages to go