How often information about backlinks updated? I didn't find any changes for last four months. Even link:mysite.com show me more links than Webmaster Tools report.
You won't ever see all of the backlinks for your site in Webmaster, many will be kept confidential. I kind of don't rely on Webmaster anymore - it takes forever to update and isn't much of a help. I just use it for the sitemap tool at this point.
From what I have read there was a backlink update recently but it sure wasn't reflected for me via the webmaster tools even though I know there were additional backlinks added from the last update. So yeah it doesn't seem to be as reliable as one would hope.