Does this work fully with 12+1 sakura 3in1 firmware?
Last time I tried was a few firmwares ago and it froze about 5mins into it.

Is that issue sorted now?

 

what kind of memory card do you have, and how did you format it?

 

Sandisk 2Gb
I don't think i've ever formatted it, used straight out of the box.

Should I be formatting it?
What with and to NTFS or FAT32?

 

I've downloaded the panasonic SD formatter.
Can I copy my data off the card, format it, then copy data back on again?

 

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.
That's it)
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)))