If you're running 6.1, yes, the tracking code is in the header, but this is by design. 6.x uses a new version of Google tracking code called async tracking.
Basically, instead of loading the tracking code in order with the page (like previous versions of the tracking code), the tracking code is loaded in parallel at the same time. A browser visiting a page with the async tracking code will load both the page and the tracking code at the same time without conflicting. This means that even if Google's servers fail, the page content will load just as fast as if the code was not even on the page.
The reason for now placing this code in the header is it increases the reliability of ensuring visitors are tracked. Previous versions of the code could miss visitors if they navigated away from the page before everything loads. Since there are no issues with slowing the page like previous versions of the code, the tracking code is placed at the top to give it a higher chance of loading before navigating away.
You can read more about the async tracking code here: http://code.google.com/apis/analytics/docs/tracking/asyncTracking.html