If you are still experiencing this issue, then I would encourage you to double check your apache aliases to ensure that they are configured properly for each and every user.
If there is a block that contains the value:
Require valid-user
Then any logged in user will have access to the directory, regardless of who they are.
Alias /USER.rtorrent.downloads "/home/USER/torrents/rtorrent/"
<Directory "/home/USER/torrents/rtorrent/">
Options Indexes FollowSymLinks MultiViews
AuthType Digest
AuthName "rutorrent"
AuthUserFile '/etc/htpasswd'
Require user USER
AllowOverride None
Order allow,deny
allow from all
php_admin_value engine Off
</Directory>
Alias /USER.deluge.downloads "/home/USER/torrents/deluge/"
<Directory "/home/USER/torrents/deluge/">
Options Indexes FollowSymLinks MultiViews
AuthType Digest
AuthName "rutorrent"
AuthUserFile '/etc/htpasswd'
Require user USER
AllowOverride None
Order allow,deny
allow from all
php_admin_value engine Off
</Directory>
Finally, please ensure there are no left over symlinks of download directories in /srv/rutorrent/home
. It’s possible a symlink here may supercede an apache config pointing at the same location.