One of the more typical questions you find in the Google Webmaster Help forums is why do not search query reports in Google Webmaster Tools look wrong.
In one explanation from a Googler, he explains how the numbers actually work. Google employee, Asaph Zemach, said in the thread:
The keywords you see in webmaster tools "Search Queries" feature correspond to the AdWords tools when you set your matching mode to "[exact]" (use the box at the bottom left of the screen). If you do that you will see that the total monthly search volume for [trading software] is actually 14,800. What the information in WMT is telling you is that of those ~15K queries, you showed up in ~2400 with an average position of 8. Given that your site ranks towards the bottom of the page, it's quite likely that under different circumstances (different users, different locales, etc) it would drift between the first and second page, so the ratio of 2400 impressions for you vs 15K global impressions does not seem unreasonable.
This may be one of the clearest and most precise answers I have seen to this question. Of course, it is pretty detailed and specific but if you read it a few times, it should make things crystal clear.
Forum discussion at Google Webmaster Help.
