There are many reports both in the Google Webmaster Help forums and WebmasterWorld reporting major drops in the number of impressions reported within the search queries report in Google Webmaster Tools.
One webmaster said:
It is showing 50% drop in impressions & clicks at search queries report. Whereas, my actual traffic is improving. Any idea is this some kind of bug or Google doing some kind of changes.
It seems a lot of webmasters are noticing the discrepancy in the Google search queries report. A preferred member responded, "I can confirm the drop too, across multiple sites. It looks like a glitch."
I am personally not able to replicate it on my Google Webmaster Tools accounts but it does seem to be a somewhat widespread issue.
Do you see this issue in your account?
Update: On February 13th, Google told me, "It should be caught up again soon -- hopefully in a few days."