One of my brilliant strategists may have figured out the discrepancy:
Why doesn't Webmaster Tools data match Google Analytics data?
Webmaster Tools data may differ from the data displayed in other tools, such as Google Analytics. Possible reasons for this include:
- Webmaster Tools does some additional data processing—for example, to handle duplicate content and visits from robots—that may cause your stats to differ from stats listed in other sources. Some tools, such as Google Analytics, track traffic only from users who have enabled JavaScript in their browser.
- Google Analytics tracks visits only to pages which include the correctly configured Analytics Javascript code. If pages on the site don't have the code, Analytics will not track visits to those pages. Visits to pages without the Analytics tracking code will, however, be tracked in Webmaster Tools if users reach them via search results or if Google crawls or otherwise discovers them.
- Some tools define "keywords" differently. For example:
- The Keywords page in Webmaster Tools displays the most significant words Google found on your site.
- The Keywords tool in Google Adwords displays the total number of user queries for that keyword across the web.
- Analytics uses the term "keywords" to describe both search engine queries and AdWords paid keywords.
- The Webmaster Tools Search Queries page lists shows the total number of keyword search queries in which your page's listing was seen in search results, and this is a smaller number. Also, Webmaster Tools rounds search query data to one or two significant digits.