ok, I have dug up some more information about the GPIO situation,
If you have a green board (revC) it does not have the GPIO expander chip (the cy8c9540a), so you only get the 16 GPIOs.
If you have a blue board (revD), then you will also have the GPIO expander chip, and you'll see GPIOs 16-55 when the cy8c9540a driver loads.
I borrowed a blue board, and sure enough, it came right up and found the additional GPIOs.
AlecH, what color is your board?