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:
So for these sites, the issue hopefully will be resolved shortly. No need to panic.
Forum discussion continued at Google Webmasters Help, WebmasterWorld and DigitalPoint Forums.