I realize I'm chiming in a bit late here, but here's what worked for me.
My setup: M3DS Real, Firmware 3.4, SanDisk MicroSDHC 6GB Class 4.
Without soft reboot, game froze during cutscene animation after first frog battle. With soft reboot, game froze upon hitting Select before frog battle.
Using WinXP, I copied all files off the MicroSDHC card to the local hard drive. Then I reformatted the card (as FAT32).
Here's the trick: First copy back SYSTEM folder, then copy NDS folder. Then copy any other folders.
I found out a long time ago that if you copy the NDS folder after other folders (like PDADS or GBA), the main M3Real screen loaded several seconds slower. By copying the NDS folder earlier and turning off soft reboot, I was able to get past the cutscene without freezes. I haven't tried the NDS folder first then SYSTEM, but that may work as well. Regardless, I have always had to reformat to get it to work (i.e. using Drive Sort doesn't help with the speed issue). As always YMMV.