Solution 1: Disable 'Clutch' mode for the stick. Issue 1: Button30 (default 'boost' in the Elite config) button doesn't work in game.
However as some of the other issues require that utility to be installed to resolve them, I am assuming you've installed both the joystick driver and the configuration utility from MadCatz' website. 2 - Some of these issues only appear if you have the Saitek Profile Editor utility installed. My solutions work even if this dialog is closed (As it should be except for when testing). This is presumably because with that open certain custom settings for the stick are overridden.
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.
