I'm not certain what determines the nested Front Matter--perhaps guide entries?? I just know it doesn't happen on all books. Most of the time, with the generic ones I build, I see "Beginning", "Cover," and "End"... with my NCX (my fully intact NCX) falling between "Cover" and "End."
Off hand... I'd say all the standard epub guide entries from the OPF (minus the cover and start/text entries) are all collapsed under the Front Matter heading. Have to do some testing, I guess. "Beginning" is clearly the start/text guide item and "End" is the "Before You Go" Amazon addition.
Sorry for the slightly less than ecstatic revelation, Hitch.
EDIT: Well some quick testing rules out my OPF guide-item guess. Back to the drawing-board.