I would venture to say that the machinery was not installed correctly. If you remember, Brown stated they were having trouble while they were still in the Yazoo. Also, consider the short amount of time that the boat was built in and I would guess that there were not a lot of qualified ship-builders in the Yazoo Delta.
Much has been made about Eads turning out his City class ironclads in a very short period of time. But I think when you consider the hardships that Brown faced, the building of the Arkansas should at least rate up there with Eads.