As Mary wrote, when Moodle restores some activities, it restores them in the same section number they where in the course when the backup was done.
That generates empty sections for you, but at the opposite, if you want to add things to an existing course with all sections already filled, it creates doubles in the sections. See MDL-61100 about that. It could also be made to answer your problem, if sections are created just when no sections are used in the destination course.
What you could try (not sure of the result) is to move the sections you want to copy in the first sections of your original course before doing the backup, and then try to restore to a new course.