Vanessa Fox at Google Webmaster Central posted a blog entry named using the site: command where she explains that they are updating the site command to make it more useful for Webmasters.
Historically, Google has avoided showing pages that appear to be duplicate (e.g., pages with the same title and description) in search results. Our goal is to provide useful results to the searcher. However, with a site: command, searchers are likely looking for a full list of results from that site, so we are making a change to do that.
So Google may soon show a full list of indexed pages soon.
This post was actually sparked by DaveN asking Who Killed SEW because a site command search on Search Engine Watch's site returned only 260 results. Danny Sullivan dug deeper and wrote The "About 260" Problem: Google Site: Command Glitch.
That all sparked the Google post explaining they are working on a new site command and that there are currently some issues that need to be resolved.
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.
Elisabeth Osmeloski of Search Engine Watch showed more examples in her Google and the Site: Command Glitch; explaining it also happens with ClickZ, 1UP and USA.gov.
But interestingly enough, there was not a lot of reports about this Google bug in the forum. Mostly, but not completely, just after the fact.
But this does go back a bit father than what is discussed above. We reported a month and a half ago that Google Seeing Sub Domains As Part Of Main Domain? Site Command Change in which Google told me they are working on the solution they mentioned above in their post. They seemed to have implemented much of it, which may have caused the issues with the "about 260" bit. In any event, Google has had issues with the site command in the past, including: