Nero BackItUp doesn't support backup hidden folders. You need to disable the hidden attribute of the folder first.
1. Open the folder Properties window. Uncheck the Hidden option of Attributes. Click 'Apply'.
2. Select 'Apply changes to this folder, subfolders and files' on Confirm Attribute Changes Dialog. Click 'OK'.
3. Run Nero BackItUp. Select the folders to back up.
PS: The system %appdata% folder is hidden by default. According to Nero BackItUp's design, Nero BackItUp doesn't support backup %appdata% folder even though changing the folder property.