First let me say thanks for adding threading support, and more importantly, thanks for sorting threads by activity. These two things really allow discussions to take on a life of their own, engaging more people, and building a sense of continuity and community.
However, there is a problem. If discussions go on for a while (which is a good thing), the threads can get rather long (naturally). Each time a very long thread gets updated, it can push all other messages of the page.
There are two common solutions to this problem:
1) A 'collapsed thread' view. The default view only shows the first message in each thread, with a [+] next to the message. Clicking the [+] causes that thread to be expanded. This is a common approach in newsreaders and mail clients.
2) A 'topic view'. Again, the default view only shows the first messages in each thread, which is now refered to as a 'topic'. Clicking on a topic takes you to view of that topic, fully expanded. This is a common approach taken by popular message board software, as well as web-based newsreaders like Deja.