Alright, I just got it, at the right time.
After some thinking, I think I may know why this glitches and how to fix it.
I noticed when I went through and finished the story, I didn't get 4 of the story achievements. I got them, once I played through those levels in Freeplay.
I think the Minikit achievement glitch may work in this manner too, but unlike the levels achievements, you can't just replay levels to get the kits again.
So as long as you have a backup save, you should have a chance to try again, and it may unlock the second time.
If this is how the glitch happens, nothing you do in the game should matter in causing the glitch, like quitting and saving, co-op, or anything else like that. It may just be an achievement glitch like the level completed achievements not unlocking.
Though I could be completely wrong, since it also sometimes unlocks early for some people. But a backup save would still be a good idea.
Last edited by Earthbound_X; 08-24-2012 at 06:56 AM.