Stupidly enough (on the part of Adobe), it seems pagination depends on the compression level of the files! I've just uncompressed your book and recreated it in two versions:
A) No compression (level 0). The cover is in pages 2-3, and the book is 56 pages long.
B) Maximum compression (level 9). The cover is in page 1, and the book is 14 pages long.
This makes the "page" numbers even more arbitrary than before
