A lot of these issue go away if the Windows Control Panel joystick dialog (where you can see which buttons/axes you are using as you use them) is open in the background. I had a fair few issues with this when I first got my X52, in that I didn't seem to be able to bind half the buttons I wanted, and others weren't showing up as I expected them to, so I thought i'd outline the issues I had here and the solutions, in case anyone else is also suffering similarly.