I did not have any trouble with transmission but found I needed to have the default rtorrent configuration file in my home directory.
Code:
cp /usr/local/share/examples/rtorrent/rtorrent.rc ~/.rtorrent.rc
I did not have to uncomment anything in .rtorrent.rc.
Also in rtorrent the downloads do not start automatically. You need to select the torrent and ^S. See man rtorrent. Lastly, there is a warning about hash checking for the BSD's. I just have it disabled.