I think you might be right about a pathing (or permissions) issue possibly related to the account under which it’s being run. When you do it on the command line is it as “you” or as “root” (which I assume is what it would run under from rc.d).
The actual path issue might be related to mono (or possibly certificates) as mentioned in these two (non-FreeNAS / BSD related) posts:
If neither of those are helpful perhaps somebody who’s already running it on FreeNAS (such as @Joe or @John_Delisle) might have some suggestions…
Out of curiosity, not including this current issue did you have any difficulties getting Duplicati installed & configured in a FreeNAS jail? I’m wondering if it needs it’s own How-To entry or not.