Before you start blaming rtorrent for not doing its job, how are you editing the default download location? If you are only changing it in rutorrent, then yes every time you restart rtorrent, the default download location will be reset to the location specified in
~/.rtorrent.rc. This is the file to edit and I suspect you haven't
However, if you have then read on.
The service file to alter would be
Easy solution would be to add a preexec command such as
wait 10. A more elegant solution might be figuring out if you can change the
after= to a more appropriate time in the bootup sequence. It depends on how you are mounting the drives though
man systemd for everything you could ever wish to know about systemd services