Ummm, I think you missed the most obvious answer, which is: They are totally two different Editions, that's why. The hard copy you have is a 2012 Edition, which by an large would have changed from the 2003 edition that e-Sword has.
It is the same with any other translation of the Bible when new editions have come on the scene, e.g., NIV 1988 edition and the NIV 2011, and you will notice the same sort of thing. So, with that, its really no biggy except when changes in the new editions are really bad. But this is not the forum to go into that kind of thing.
Blessings,