If it's NOT showing that message, then it probably has to do with some of the emulator settings. However, seeing as I don't use an emulator for the carts (only colo/XD), I can't really help you much more than that, sorry :/
Hi Zari, I try make the palpark glitch on emulator for use the palpark multiple times, but when I change the time of my PC not shows the msg of: "You are using a different Nintendo DS, or its internal clock has been altered. If the game's time setting is changed, you will not be able to migrate Pokémon for another 24 hours. Would you like to change your game's time setting to match the Nintendo DS?" You know the reason?