So I have a black Gamecube and a Mad Catz controller, and I'm having issues with certain games. I can play Wind Waker and Metroid Prime and the controller works just fine. However, when I try to play Metroid Prime 2 or Twilight Princess, the analog sticks refuse to work. They work absolutely fine in WW and Prime, but they do absolutely nothing in these specific games. I've Google'd it, but apparently I'm the only person who's had this problem to this point. Can anybody shed light on what might be the issue here?
Unfortunately, the issue is likely that the MadCatz controller is dying (their parts are bargain brand, and their soldering is a joke). If you have access to a confirmed working 1st party controller, I'd advise swapping it out for a play session and seeing if it works.
I wish I could be more helpful or specific than that, but what I can say for certain is that the 1 year failure rate for MadCatz controllers among me and my friends is 100%, regardless of system. While I have not personally seen a MadCatz controller lose analog stick function on certain games, I have seen them lose function on a specific button on certain games numerous times.
You could attempt to bring it to a store that does controller repairs, but it would likely be cheaper at this point to purchase a lightly-used 1st party GameCube controller. Honestly, I'm beyond surprised that it's 2013 and you have a working MadCatz controller for the GameCube at all.