Some evil ISPs implement traffic shaping to specifically limit BitTorrent bandwidth. This brings slower downloads to you and your peer.
All modern BitTorrent clients have encryption capabilities but most of them came disabled by default.
Please configure your client to encrypt connections. You will have faster downloads even if your ISP does not limit your traffic, but because your peer’s ISP does that.
By the way, today I started to use the ultimate BitTorrent client for Linux, BSD and UNIX: rTorrent. It is text and console-based, superlight, superfast, runs very well in my K7/192MB machine, accessible from anywhere through SSH and a screen window.
To install it:
Debian: bash$ sudo apt-get install rtorrent Fedora/Red Hat: bash$ sudo yum -y install rtorrent
To enable encription I added this line to ~/.rtorrent.rc: