ANSWER: I do not think that books were left out from the Hebrew version but rather books were split up and listed separately in the King James Version Bible. They were subsequently arranged in the same way as almost all modern translations of God's word.
Ezra, who originally canonized the Old Testament, had twenty-two (not thirty-nine) books in it - the same number as letters in the Hebrew alphabet. What we today consider four books - 1 and 2 Kings and 1 and 2 Samuel - were originally inspired to be a single book. Also considered only one book were Joshua and Judges, Ezra and Nehemiah, 1 and 2 Chronicles, and the writings of all twelve of the minor prophets. Rest assured, though, all of the characters have been accounted for and that is what is most important.
Mordakhai Joseph, who does an excellent study of the Old Testament, reads from a Hebrew to English Bible. I've noticed in his audio lessons that his Bible does not always follow the same chapter or verse patterns as my King James Version. He has to keep giving us updated references so we can read along and not get confused. So I suspect that the language syntax of the Hebrews has something to do with it as well. Hebrew is written from right to left and in all capital characters which might make an exact match impossible as English takes up several words or sentences to explain the same meaning.
It was not in the original manuscript to even have chapter and verses designated. That came much later when men copied them and added it for clarity and to know which lines they were on. In the original Masoretic manuscript each Hebrew character has a number designation and each word and line must add up to a certain original sum or the whole copy was thrown out. This is how we know that the original Hebrew has been copied correctly for thousands of years.
There are not only differences in the number of books but also in their sequence. We know that in the New Testament Greek that Apostle Paul's epistles should follow the general epistles of James, Peter, John and Jude - but they are reversed in the KJV. And in the Old Testament we know that Ezra, Nehemiah and Chronicles were the last books written in historical sequence yet in the King James Bible they are placed in the first third of God's word. This confused me until I understood this and labeled them in the right order.