I've enabled the option for site to site transfers in the client (LE version, build 1441) but have been unable to do site to site transfers.
Apparently what occurs is that both panes end up with control of the most recently connected server.
I am accessing two SFTP servers simultaneously (or at least, trying to) so perhaps this is a limitation of hash keys and SFTP? I will try the newest build tomorrow and see if it makes a difference.