I get the same thing. I have a Joomla site with location listings and when watching live, Woopra correctly shows the visitor actions - i.e. where they go on the site. However, if I use search to view past visitor actions, it shows only that they went to the main page or one of my other pages (though it shows that page as index.php). For instance, today it shows all visitors going to the "Find a Historic Site" or "Grissom Air Museum" pages. I even went to other listing pages to test it and they all showed "Grissom Air Museum".
The name of the page shown (in this case Grissom Air Museum) seems to reflect the last Query item from the Dashboard. This morning, someone ended up on my site by searching for Grissom Air Museum. Another day, the last query was "Old North Church". So every action on the Search tab showed visitors all went to the "Old North Church" listing (even though it showed the URL as index.php).
I hope this makes sense. If you need more details, let me know and I'll try to provide.