Most likely you have the SVN version, and in that case do this as the root user:
Code:
sudo cd /var/rutorrent/rutorrent
sudo svn up . plugins/*
You may also have to clear your browser's cache and restart it. If it doesn't say ruTorrent 3.3, then your browser is still using the old files.
Another thing, you should restart rtorrent:
Code:
sudo /etc/init.d/autodl_YOURNAME restart
Replace YOURNAME with your user name.