I just had the exact same problem after running box upgrade.
However, my /srv/rutorrent/home/db/master.txt contained the correct username, but the /etc/apache2/master.txt file was empty.
I solved it simply by overwriting the empty one with the okay one and running upgrade again.
cp /srv/rutorrent/home/db/master.txt /etc/apache2/master.txt
Did not even have to restart any services, everything started working instantly.
A suggestion to devs - maybe the updating functions could do a sanity check, by comparing the variable with an empty string?
ziagl, this might not be the best way, but I’ve had some luck troubleshooting rtorrent, by using sudo to get a shell for the seedbox user and running rtorrent manually.
sudo -u USERNAMEHERE bash
Then, hopefully, it will give you a helpful error message, that can be researched further.