Forum Moderators: Robert Charlton & goodroi
i did a backlink check on my site and it shows a ton less links then webmaster tools. A thousand less actually.
Usually the backlink operator would show the same amount of backlinks as Webmaster tools and today it seems messed up. I havent dropped in the serps yet but it worries me of impending doom.
Your "real" link numbers (and PR as well) are not being reported directly to you from the currently active data that Google uses to calculate search results. Instead these report numbers are exported every once in a while from Google's "back office" where such data is continually updated.
In other words, a real change would show up FIRST in your rankings. Then only later, and usually much later, you would see it in the reporting features such as GWT, special operators and/or the toolbar.
Now about the difference that just showed up for you. Since March 2007, it has been common for GWT to show more backlinks to the authenticated owner of a site than are shown in the link: operator data which is avaialble to the general public.
So I'd say this is not likely to be a portent of any real trouble coming for your domain. It's most probably just a reporting oddity.