This may be an example of a known problem.
When EA first creates items in a Package, it doesn’t put them into the database with sequence number (1st, 2nd etc). Somehow, the EA UI seems to make it all OK.
Elements only get a sequence number when you change the order.
So, just move one item up the list, then back again, and EA will create an explicit sequence in the DB, which eaDocX can pick up.