Can you believe, recently I got a result by observing a site indexed without “WWW” even that site “http://example.com” is being redirected to the http://www.example.com?
What I believe is that the URL might be encoded in web page information are published as 'http: //example.com' rather than 'http: //www.example.com', and since now Search engines has been removed that particular Domain, by the parameters set by Webmaster Tools, it's difficult to set the best preference of the URL. Although Some Webpages are listed with "WWW" & some are listed "without WWW". Now I think that it's not a problem, but it can lie down site rankings.
But soon I got the solution; you need to add this kind of site to your WMT account, just click on the settings icon and select the option “site setting” there you will find the option how to set up your domain prefered.
