The other day, Google released a redesigned Webmaster Tools area. Soon after it was released, webmasters began noticing that the linkage data found in the new Webmaster Tools was out of sync with the one found in the old Webmaster Tools version.
Google has confirmed the issue, saying:
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.
So for these sites, the issue hopefully will be resolved shortly. No need to panic.