IMHO, I think Hiro's malfunctioning abilities have to do with the fact that he was permanently depowered and then artificially rebooted via the omnibaby. I think Hiro's body cannot support his former powers again because he is missing the genes that produced those effects. Of course, I wouldn't count on such brilliant explanations from the writers themselves. I mean, they've proven that they can't write good continuity.

Think about it. Matt's baby can give life to inanimate objects, making them act the way they are designed/constructed to do. I.e the toy cars and planes, which are supposed to fly and such, and so the baby's powers made them. Hiro is the same, albeit he's organic and much more annoying. His original DNA was built to time travel and manipulate time. But he doesn't have that "X-gene" anymore.