Both articles state that the researchers were arrested for stealing (or taking possession of) a voting machine. Quote from the Wired article: "Halderman says the researchers believe the person who gave them the voting machine had legal access to it and provided it in the interest of transparency and scientific study."

That's a little different than being arrested for finding bugs in the software or hardware. Prima-facie, it does seem like stealing government property without proper written authorization. Arrest still seems excessive, but the circumstances seem to be a bit more nuanced.