This could have something to do with either a bad torrent corrupting your settings (task namely) or where the torrent is attempting to extract to… only thing I can think of as the upgrade does not alter permissions with good reason.
Are you trying to extract outside of the users /home/< username >/torrents directory?
If not, try to make a quick backup of your settings and see if the issue lies within a bad torrent. You can do that by doing the following:
cp -a /srv/rutorrent/share/users/< username >/settings /srv/rutorrent/share/users/< username >/settings.bak
then do a restart of RTorrent, either from your dashboard or by doing
systemctl restart [email protected]< username >.service
Updated the backup command as I only gave you half the command.