What is the new commandment and how has it been true from the beginning?
I assume that you are talking about the one commandment that is left by the time the pigs get through with things. This is seen towards the end of Chapter 10. The commandment says that "All animals are equal, but some animals are more equal than others."
This has been true ever since the beginning because the pigs (and to some extent their enforcers, the dogs) have been more equal ever since the beginning. Even at the very beginning, only the pigs have ever had leadership positions. At Old Major's speech, it is all pigs in the front row. Soon after the revolution, we find that the pigs are not really doing any manual labor and they are having the easiest lives -- like getting the milk the hens used to share.
So the pigs have been on top from the start.
Some of the Animal Farm animals seemed to remember that changes had been made to the original commandments, but the pigs assured their comrades that nothing had really been altered. Originally there were seven commandments, but eventually every single one was amended by the pigs. The most important was the seventh: "All animals are equal." In the end, there remained only one commandment, and it, too, had been changed. It now read "ALL ANIMALS ARE EQUAL BUT SOME ANIMALS ARE MORE EQUAL THAN OTHERS." This commandment had always been true, since from the start, the pigs had abused their rule of equality, always maintaining an upper hand over the others.