The FAT driver in original SYS is known to be buggy.
If you feel like experimenting, install this and then format your filesystem:
https://github.com/PetteriAimonen/AlterBIOS/downloads
That replaces the filesystem driver with elm-chan fatfs. It’s still very experimental, but if it doesn’t work just reinstall SYS to get rid of it. When it works, the boot screen will show “AlterBIOS: Ok” on the top row.