Because the traffic shaping rules to limit BitTorrent throughput cover the same range of ports MSN uses. Magic Shaper uses 6881-6999 to classify BitTorrent traffic, which encompasses the MSN ports 6891-6900. You can change the rules that classify BitTorrent traffic in the traffic shaping pages.

Note that bit torrent traffic is now all over the port list, including well known ports like 80 and 443, so this option can just be disabled with little real consequence.