Deja Dup (Backup) Not Ignoring Folders
I never did figure out why folders were not ignoring properly. However, I went back and selectively chose which folders to backup, rather than select which ones to ignore. In other words, I setup a whitelist to backup rather than a blacklist to ignore.
This isn't really an answer, but a work around that gets the job done.
You might want to check your backup files directly. Have a look at this bug
https://bugs.launchpad.net/deja-dup/+bug/514931
looks like directories are listed, but not backed up.