How Accurate Are Clickthrough Stats In Google Webmaster Tools?

[passmaster16]

I have a site that I've been tracking with both Google Analytics and Google Webmaster Tools for about a year now. One thing that I noticed in WMT is that while I have a decent number of impressions showing, it rarely shows any clickthrough for those impressions. Usually the only clickthough I see is for one or two searches on my organization name. Yet when I hop over to Analytics and go to Traffic Sources>Search Engines>Google, I see a substantial number of keywords that produced visits. When I do a comparison of the Analytics results vs WMT for a particular month, Analytics shows much more Google keyword traffic. Is there something wrong or am I just misunderstanding how Analytics results differs from WMT?

TIA
Josh

[tedster]

WMT stats are pretty rough and buggy. Analytics is much more dependable.

[icedowl]

WMT stats are pretty rough and buggy.

That's putting it nicely, Ted. Perhaps too nice! My WMT shows very few clickthroughs, but when I look at my Awstats or Analytics I see a constant parade of visitors for the very terms listed under impressions. I wish they'd get it fixed so it works correctly.