ry logging rtorrent's actions to see if this is really an rutorrent issue
log.open_file = "rtorrent", ~/.rtorrent/logs/rtorrent.log
log.open_file = "torrent", ~/.rtorrent/logs/torrent.log
log.open_file = "tracker", ~/.rtorrent/logs/tracker.log
log.add_output = "debug", "rtorrent"
log.add_output...