Well, I've run into something interesting. Been at this for a few days, and it seems that something has permanently removed Luigi's Mansion and Mushroomy 1-1 from my available stages. As in, attempting to load them with freeze the game, even when no codes are active and the SD Slot is empty.
So I figure something must have saved itself onto my harddrive that ought not to have been saved. And the odds of this being able to be fixed without losing the save file are slim. but I obviously want to know what happened.
I don't think I've used any codes other than ones posted in the list thread, and haven't used any of the ones which alter the stages. I've tried not to save a lot of things. There's been standard autosave match data, a trophy and some stickers, the final challenge unlocked (take that Intense Boss mode), a whole lot of snapshots (free camera is the greatest thing ever), no custom stages, and a single replay that a friend tried to save but didn't appear when we got around to checking the replay screen for it (after the codes had changed).
I figure the Replay is the most likely problem, but I'll list codes in case you recognize something as faulty.
(Color/Size/Character Modifiers including alloys, no entrance animation (for the alloys), Infinite jumps and Up-B's, Unrestricted Pause, Control Loser on victory screen, More than one FS, Taunt enables FS, Item spawn rate, aggressive pokeballs and AT's, and "infinite Smash Balls and pokeballs" (not really sure what those ones DID), and Super Captain Falcon)