As I reported yesterday at Search Engine Land, the site command may be a bit buggy for you right now and may not be resolved for about a week.
In short, some SEOs and webmasters began noticing that conducting a site command in Google for large sites would only return 30 results. I personally have not been able to replicate it but I've been getting random complaints about this on Twitter. Justin Briggs has a screen shot showing this in actions, where a site command for amazon.com only returns 30 results.
Google's Matt Cutts told us at Search Engine Land:
This is a temporary side effect of the domain clustering change that I mentioned in my video. We expect that site: will be back to showing lots of results by sometime next week.
The domain clustering change was something Matt announced last week in his ten SEO changes coming to Google.
So don't panic, your site is probably still indexed by Google.