I'm not sure if this is right, but the discs have different GAME IDs? To check, open CWCheat while running the first game and right down the string of numbers you see at the top. Do the same with disc 2, then compare. It could be that they require different sets of cheats, because they way CWCheat works is by changing values of strings loaded into memory when you play a game. The strings are called "addresses", and they could be different for each game.