HELLO! I'm using USB Loader GX.
I understood that you had to start a save file on MP1 before MP2 and MP3 worked. I saved at the beginning of MP1, and tested the other games, and like it was said they worked just fine.
I've been playing MP1 for like the past week, and yesterday I beat the game with about 88% items found. It said "Do you want to save your game? If you save, you will end your game and a new game will be started." I said "No, i want to find 100% items and play around with it more!" The screen went blank and took me back to the Wii menu. With USB Loader, MPT just goes straight to the game, and you have no access to main menus or anything, so I just interpreted that as the point where it would normally go back to the main menu.
I tried to start it up again, and it went to the beginning of the game, as if I had no save file. I confirmed this fear by trying MP2 and MP3, which wouldn't start. Trying to cut my losses and saving a new game from the beginning of MP1 doesn't work either - when I restart it goes back to the beginning of the game.
In my Wii savegame manager, I don't see MPT save data anywhere. However the first save square is blank, and I can't select it. Running Savegame Manager from HBC reveals there's a messed up save file called "-%'! -!. ↓". I tried deleting "R3MP" in Anytitle Deleter to start fresh, but it still doesn't seem to work. What is going on? Does USB Loader Metroid Prime Trilogy save special files that I'm not seeing?