Do you have your website listed as either
www.yoursitename.com or yoursitename.com?
If you only have one of these then put the other one in as well, they read as two different sites to Google, it's the same on one of my sites, no data for the one but lots for the other.
This is probably the reason. I think they now ask which method of presentation you'd like to use these days (I'm told using the www. is preferable) and the one you have chosen will be the one with all the data.
There is a delay in the processing of that data though, I think it's only a week or so behind. If you still don't see results and you're certain you are getting organic traffic their forums are the best place to look for a solution.
I don't see how you could have Google showing as sending you traffic in Analytics without there being keyword data in Webmaster Tools.
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