[DS] Some Homebrew Causes File System Errors

Hardware: M3 (new MiniSD version [with the clear-grey casing]), NDS (v1 with FlashMe), KingMax 2GB memory card (Formatted with FAT16 with the utility from sdcard.org)

Why is it that some homebrew (NetHack, DSOrganize, stuff that writes to the card) causes my card's file system to become corrupted? When I say corrupted, I mean folders with junk contents, bad files, files don't even show up sometimes, and existing files are corrupted on the card occasionally. I end up having to reformat my card to fix the problems, so I just stopped running those homebrews.

Is this a problem with my M3, or is my card not supported by libfat? I can't find a libfat compatibility list anywhere, but the M3 is supposed to support it.

Thanks in advance for any input,
Githlar