If you noticed that Google has a new look coming for Webmaster tools you will also have notice there is external backlinks data is different in new vs. old (or current) webmaster tools.
Google is about to release a new version of the Webmaster tools and at first glance you will notice that the external links in the new version are much lower than in the current version. After some research we found that the problem has been answered by Google at this link and states the following:
“We hope you’ve had a chance to check out the new, redesigned version of Webmaster Tools! You may notice that your backlinks data differs between the new and old versions—this is because we’re still filling in data for some sites in the new version. We hope that you’ll find the new data more comprehensive once it’s 100% filled in.”
Based on this it would appear that it is only a matter of keeping an eye out on this as Google makes sure the data from the current version ends up in the new version.
Hopefully this will help clear up any issues with others as they find this problem. Thanks for checking in at SmartFinds Internet Marketing.