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. Typically BitTorrent only uses 6881-6889.
Credit: Chris Bagnall