Questions that are only in the context of a specific quiz are not backed up by the automated backup. I've attached a manual backup and automated backup of the same course. Whether the question is in use by the quiz or not doesn't seem to matter. (If the question is in use, then it triggers MDL-16275 when restoring.)

To create this problem, add a quiz to a course and in the quiz. In the question area, choose the default category for the quiz (I believe the default category is the default for the class). Create a new question (type doesn't appear to matter) in this category. Allow the automated backup to run. If you look at moodle.xml in the backup, the question won't be there. If you do a manual backup from within the couse, the question will be backed up properly.