I downgraded to 1.2 (erased utorrent.exe, erased file associations, erased %appdata%\utorrent folder, then erased every instance of utorrent i found in my registry) and i didn't have any problems with multiple instances. i then let it upgrade itself to 1.3 and the multiple instance problem started happening again. It's also being discussed in troubleshooting forum: http://forum.utorrent.com/viewtopic.php?id=3164