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.
Forum discussion continued at Google Webmasters Help, WebmasterWorld and DigitalPoint Forums.

Comments:
diarmuid ryan
05/15/2009 10:18 am
well, thats a relieve, i thought my site had lost over a thousand links! phew!
David Corman
05/17/2009 11:35 am
I recently noticed that some of our clients' backlinks were not appearing in the old version of Webmaster Tools. Do you know why this might be?
hgil
06/19/2009 12:36 pm
I wished they didn't change anything. Google Webmaster tools was near perfect before. They've altered the way keywords are presented now to us. Before we had 2 sets of data: 1. keywords found in your website 2. keywords found from external links Laid out neatly, side by side. But now we have only one set.
Amit Sati
08/03/2009 05:51 am
This information seems to be quite a relief for all webmasters like me, however I still believe Google should hurry up things, because end users may not get precised results in this transition period.
Eko Dost
02/05/2013 08:38 pm
I am having the same problem right now. I hope it will be solved shortly.