Must be your cheats that are wrong or something, double check because some games need different cheats for different regions of the same game.
I just tested a cheat.gct with Mario Sunshine and named the game as the ID and the cheat file as the same in the same folder and it worked.
I use USBLoaderGX
I let USB Loader GX download the cheat files. I can't get any cheats to work for Mario Kart Double Dash or Luigi's Mansion. Both are NTSC games.