As of at least Unity3D 3.5.6, I haven’t been able to get a joypad to work with scrolling a menu. I’d spent many hours trying all kinds of trickery to get it to work logically: I rationalised that I must surely be at fault, not Unity3D.
Turns out Unity3D really does have a problem with this particular issue, and I don’t think there’s an elegant solution. No doubt it’ll be resolved in future releases.