BitTorrent itself, imo was the absolute pits. It was hellishly slow (I have 1Mbps broadband), and you couldn't even pause the download or minimise it to the system tray. This was the latest version, btw.
After discovering just how awful it was, I tried Shareaza's built in BitTorrent client, it's so much faster (even by Shareaza standards; it sure ain't the quickest) and finds more sources. And it can be paused, and minimised to the tray.
Try it instead.
Master of common sense. If you don't like it, stop reading.