We have tried it on an original NDS with a flashcart and still had the same issue, so I don't think model makes a difference, but thank you for the kind offer!
Well, tested Jpns version and it's does not freezeUpdate: We've tested the special message on another 3DS running custom firmware, (newly installed, default settings), and everything ran as expected, leading us to suspect that it is a flashcart firmware issue. Unfortunately, there isn't much we can do in this case, other than advise anyone experiencing the same issue to try using an emulator, or, in the case of playing on a DSi/2/3DS, load the game directly from the SD card. We apologize for any inconvenience caused!