Download links (.exe) don't get tagged on my site running WP 2.9.1 and 3.2.5 of the plugin.
My footer.php calls wp_footer() and I've tried when logged in and not logged in. The tracking code gets added, but links don't get tracked.
I might be misunderstanding things, the downloads are on the same domain and are linked to using relative paths. Could this be the problem? - Does it only track external download links?
The URL of a page with a download link is http://davehope.co.uk/projects/product-key-finder/