What I notice in ATW is that it seems to include all the links to the domain, no matter what page they are linked to.
For instance if i look for
in google, it might show me 100 links.
if i did another search at google for:
i would possibly come up with another set of external links that don't show up in the first search, and the ones to the main domain don't appear.
Now, the thing is ATW seems to include any link to the domain:
link:penguin-foobar-widgets.com includes links to
So, depending on your site, this might have something to do with it.
For instance I run a site that has nearly every page in the yahoo directory and DMOZ (each page of the site has a biography of a celebrity). A site with a lot of links from sites to different sections will appear much differently between the two search engines.
What should you do? Make a web directory based on all those 71,000 sites that link to you, so that they get a PR boost, and then when you are PR9, please link to me. :)
$#@$@# typo edit.