It honestly does sound like your ISO is messed up or if you're trying to use alt. dol files those are corrupted. Someone said before you need to use alt dol files for metroid so if you aren't already using them try finding them and loading those through GX and see if that helps. I'd also suggest trying uLoader as a pre-launcher type of thing. Use it to load games you can't normally load then once you've got some save data created with that go back and load the games through GX (might help with metroid, if you can get in-game w/ 2 or 3 you should be fine to run through GX afterword).