When Sakura boots and runs DiskCheck, it will halt booting if it finds a corrupt file. After backing up your files, try formatting your MicroSD card to FAT32, then copy just the SYSTEM folder by itself to the root of the card (don't copy your other backed up files onto the card yet). See if you can get Sakura to boot with just the SYSTEM folder on the card. If it runs, start copying your other files back over. If it stops booting after you've copied the rest of your files, it means at least one of your folders contains a file that M3 Sakura "doesn't like." You can look for the file using Windows CheckDisk, but if that doesn't work, you'll have to isolate and remove the problem file through trial and error. If you don't want to search for the corrupt files, you can back them up, delete all files except for the SYSTEM folder from the card, boot Sakura, disable DiskCheck through the GUI settings, and copy all files back.
More often than not files (particularly saves) can get corrupted in the folder that contains your NDS ROMs and .sav files, and this can lead to Sakura hanging during boot-up. Follow these instructions if you suspect corrupt data in your NDS ROM folder:
1. Remove all .sav files from your your NDS folder (back them up).
2. Delete all .cht and .opt files (you don't have to back these up, they have nothing to do with your saves).
3. After removing your .sav files from the folder, try to boot Sakura again.
4. If it still hangs, you have a corrupt ROM. If it boots properly, you have a corrupt .sav file. Skip ahead to step 6.
5. If you suspect a corrupt ROM, check the CRC of your ROMs with a ROM manager like NDSCrc, RToolDS or Rominator. If you don't use a ROM manager, you can still check the CRC at ADVANsCEne. Do a search for any ROM and check the CRC32. You can view the CRC of the ROM you have on your card by compressing it in a ZIP or RAR file, then viewing the archive. If the CRC of your ROM is different from the CRC on ADVANsCEne, it's either a bad dump, it was trimmed, patched, or otherwise altered from the clean dump. Get rid of the ROM with the bad CRC and replace it with a clean dump.
6. Check all your .sav files and make sure they're all 512KB. If you find one that's not 512KB, it's probably corrupt.
7. If you can't find one that's different from the rest, you can run Windows CheckDisk on them (or Mac equivalent, maybe DiskFirstAid will help).
8. If CheckDisk doesn't turn anything up, start moving the .sav files back onto your card five at a time, booting Sakura between each move.
9. Once it hangs, zero in on the five .sav files that caused the freeze, and isolate the one(s) that caused it