A quick review of a site with 8500 URL's I watch in Google webmastertools, and then with the use of the site: tool [ e.g. site:yoursite.com/ ] shows a huge discrepancy on recently relaunched site. 1250 v 8500 URL's. Then as I progress through the pagination the site:tool reduces to around 200 URL's.
Another look at the site:tool like this [ site:yoursite.com "unique keyword" ] to every URL shows a far reduced amount from the 8500.
I guess there have been times when the site:tool has been labelled unreliable.
Is there a lag in WMT? Do you still use site:tool for providing insight and does it provide an additional understanding of visibility and indexing.