I have installed duplicati on a Zentyal 5 server ( based on ubuntu 16 lts). It backs most stuff up great however it won’t backup the /home/samba directory.
I have added my user to the root group however it won’t read the directorys even though the folder is owned by root and group permissions are domainname\domainusers.
I tried messing about with the folder permissions however I had to revert back as it messed all the domain users share permissions up.
It sounds like you’re in the right track, though I think you might want systemctl enable Duplicati for it to start even if nobody is logged in.
I could be wrong but it sounds to me like you might be running it as a service but it’s only started after you log on so might be running under your account.
Did you set it up on your own or follow a ride here such as this one?