Did you solve the problem?)
If not, use the method, gosp suggested.
It worked for me. (By the way, I've got an 'old-revision' M3DS Real card & 4Gb C6 Transcend flash)
Start the game. as soon as the video (where Neku runs/your console freezes) starts - close the DS for about 5 seconds.
And I didn't get any other 'freezes' than in the very beginning.
(there was one long video, where I was afraid it could freeze, but it didn't)))