I’m looking for a setting or a log file or something, and not finding anything. I managed to get logging turned on for rtorrent, hoping that it would show the autotools output in there, but no cigar.
Should be within /srv/rutorrent/plugins/autotools/config.php you’ll see a line such as ::
//set true to enable debug output
$autodebug_enable = false;
You know what to do 
Just found it! And that helped me resolve my issue as well. I still had my old /media/data1 directory listed in .rtorrent.rc. Once I changed it to /home/shreezbot/media/data1/rtorrent/seeding, it started working like a champ. I didn’t realize the user accounts were jailed to their own home directories. 
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