I noticed whenever I had to reboot or refresh rtorrent ( when disk gets full) auto-tools stops moving completed downloads to the specified folders.
At some point I do something to get it working again (never quite sure what) , and once I do it works finer until the next time I have to restart.
My folder are different than the initial ones I used when installing QB. Seems to have started when I changed them. So I figure there is a conf that I need to edit maybe?
Google the crap out of this problem and i seem to be the only one with it.