Alright, back with another thing that's baffling me.
I have three sets of games that have the same title ID as the other one somehow.
-Castlevania: Order of Ecclesia/Harvest Moon: Grand Bazaar
-Dragon Quest Monsters: Joker/Dragon Quest Monsters: Joker 2
-Rune Factory 1/Rune Factory 3
This causes a problem. Let's use Rune Factory 1/3 here as an example. If I install, say, RF3's CIA first, then go to the Home menu, everything is correct. Correct icon, correct box art, correct game. Then I install RF1. I go back to the Home menu. There's no new icon. But if I select the icon for RF3, the box art shown is now RF1, and if I launch it, the game is RF1. Except for the icon, RF3 is entirely overwritten in the eyes of the 3DS and isn't installed.
How fix?