Two comments.
In your configuration.php you need to turn logging on.
change the ‘false’ to ‘true’ in the last line
$shortstat = true;
Second, it doesn’t matter if you put the include in your header or footer. It would matter if the logging required a separate page request from the client (like including an image in the page), but it doesn’t. Shortstat is entierly server side, and will not display to your page, so no need to wrap it in a div block and put at the end of the page.
As for ShortStats not being improved, I have a sweet plugin that i’ve added. Just drop a few files into your shortstats folder and check it out. (end shameless plug)
Pathstats – ShortStat plugin
