Hello. I have a site two months old and I am facing some problems indexing. If using the site: exemple.com - I 100 Results If you read the Google Webmaster Tools - I have 261 of 288 links indexed What makes this difference?
Off course: In Google results It will only show those sites which have High PR and those sites which in reality effects your sites PR ...Those Sites shown in webmaster includes all the sites - any place you dropped your link or you made any post, those links did not effect your site PR..If you check out on yahoo back link checker you would probably get shocked by watching almost 2000 (Assumption) backlinks for your site..
Your site shows 100 pages when searching like this site:example.com please try site:example.com/* once you may get result that shows less then 100 pages even. Webmaster tool shows 261 to 281 pages,so finally the reason for happening this is that WebMaster Tool shows all the indexed and yhe pages which are in sandbox too and typing site:..... is showing the result of only those pages which are actually crawled and indexed. Thats why your results of pages vary in Google and Google Webmaster tool.