I have Duplicati running on FreeNAS 11.3-U5 and doing about 85% (now 95%) of what I ultimately want it to do. The root (almost literally) of the problem is that Duplicati is running in a jail and needs appropriate permissions to access things outside of the jail. Since one usually wants to backup things outside of the jail, one has to set things up accordingly.
You may find the thread about FreeNAS jail permissions helpful.