tedster - 3:19 am on Aug 2, 2010 (gmt 0)
The Webmaster Tools reports rests heavily on Toolbar data, so if your site has lots of users on slow connections that might be an influence. Still, I would "hope" that Google sees which toolbars are on slow connections and normalizes that data.
Lots of people have mentioned that the WMT data seems funky to them. It's a good thing that it's not a big part of ranking right now!