Sorry for the late reply but I took advantage of Easter time to take a few days off.
Initially when you ran Déjà Dup under your own account there are a number of (system) files that don't back up successfully due to a lack of permissions.
Déjà Dup needs to be set up for the root user. You can either do this by logging in as root if you've enable such a login or if you haven't made it, use gksu as follows to configure the storage location:
Then add/remove directories as you require.
You can find some good pointers here and here.