Backup /etc/ as normal user Deja Dup?

Solution 1:

If your purpose in backing up /etc is just to protect against accidental error, consider using etckeeper to store it in version control. Install the etckeeper package, which will automatically set it up, and will automatically commit configuration changes. If you need to revert an erroneous configuration change, use sudo bzr on the /etc/ repository.

Solution 2:

Not sure if your problem persists but I add what I see on Ubuntu 14.04 for completeness.

I can easily add /etc to my backup locations in deja dup and it does get backed up. However, there are folders that are not readable to anyone other than their owner, which makes sense e.g. for certain system services, user passwords or private encryption keys. It is not advisable to change their permissions to e.g. group or even world readability as this would lower your system security. For some files that have a limited group readability it is possible to add the users that need to backup them to the corresponding groups, like shadow, but that I still would not recommend. After the backup finished, there will be a screen showing the files that could not be backed up which you simply have to confirm every time.