I know I shouldn't expect data from WMT and GA to match up perfectly, but this is just too weird.
There are four reports I run every Monday morning that involve exporting the top 50 organic keywords sending two of our sites traffic every week -- there's one report for each site for the top 50 and another for the top 50 with branded keywords filtered out. The vast majority of our organic traffic comes from branded search and a lot of my work at this new job is going to involve improving our traffic for the non-branded searches, so it's important for me to keep an eye on them, even though none of my recommended changes have gone into effect yet.
So this morning I'm looking over the data since the beginning of the year, and there's a particular keyword that's been showing a pretty steady rise in traffic. It's shown up in the top 50 non-branded list every week. It's been doing well enough to even make it into the overall top 50 for the past 6 weeks. The attached screen cap shows the rate of growth (I've left out the numbers and the identity of the keyword itself).
As I mentioned, I can't take credit for the improvement in traffic for this keyword, since nothing I've recommended has actually gone live yet. But I wanted to see what's been going on for my own edification, so I popped over to Webmaster Tools to see whatever I could find out about impressions, rankings and click-throughs for the keyword. It's not in the top 50 for the past month. It's not in the top 100. I opened it up to the top 500 and there were only 499 keywords returned. It's not on that list either. So I expanded the date range to cover all of 2013 so far, and I finally managed to find it in the list.
According to Webmaster Tools, the keyword has had less than 10 impressions, less than 10 click-throughs, and an average rank of 250 from January 1 to March 11. GA tells me its worst week this year had significantly more click-throughs than that, with a total YTD in the thousands. This is in Traffic Sources > Search > Organic. I'm sure I'm looking in the right place.
So how is it possible to see such a giant gap between the figures?