I believe that you have to make sure the pen touches first. Then it disables the buttons.
However it would be great to either lock the buttons, OR (even cooler, as mentioned in one of the reviews I saw) have the buttons reversed depending on rotation; i.e. when in portrait mode, have the buttons up on the left side out of the way, but easily touched by your left thumb. Then you get easy access, and they are out of the way.
I'm going to see about putting in a request over at XDA about that, head on over and request too and maybe we can get something written.