“When would one be native-born but NOT natural-born?”
There isn’t a time. The use of two terms in a manual does not mean there are separate meanings for each one. Nor does a State Department manual override the US Constitution. One is either a natural born citizen, or a naturalized citizen, or not a citizen at all.
Have a look.
http://h2ooflife.files.wordpress.com/2011/04/8_types_of_citizens-33bw2.jpg
http://h2ooflife.files.wordpress.com/2011/04/types-of-us-citizenship-ds.jpg
