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Run "gw3ds.exe scan x:" (where "x:" is the driveletter of your GW3DS microSD card) from a command prompt window to scan for problems. Run "gw3ds.exe fix x:" to fix fragmentation errors and missing game icons.
- You receive a fragmentation error when the rom file has more than 32 fragments.
- You receive a fragmentation error when the rom file occupies either of the last two clusters on an exFAT partition.
- You don't see all game icons if the root directory entry is fragmented.
EDIT: Avast seems to think that my program is infected with malware. I can assure you that it contains no malware. I wrote and compiled the program myself. I reported the false positive to Avast so hopefully they will fix it in their next virus database update.