I figured it out. In your rtorrent rc file (~/.boxee/UserData/rtorrent.rc.linux), change this line:
Code:
on_finished = move_complete,"execute=/bin/mv,-n,$d.get_base_path=,~/.boxee/downloads/ ;d.set_directory=~/.boxee/downloads/"
to:
Code:
on_finished = move_complete,"execute=/bin/mv,-u,$d.get_base_path=,~/.boxee/downloads/ ;d.set_directory=~/.boxee/downloads/"
Basically you're changing the option to the move command from "-n" to "-u". "-n" is valid on Mac OS X but doesn't exist on standard GNU mv.
After you do this, kill rtorrent ("killall boxee-rtorrent") and restart boxee to start it up again. Your old completed torrents will stay in .tmp but any new torrent that finished should move to ~/.boxee/downloads correctly.
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