The VFAT errors with Windows 98 and ME generally refers to jacked up system files or registry keys that would be very hard to pin-point andd more importantly would not necessarily prevent the inevitable outcome: complete operating system crash.
If you do not have a valid system restore point or a registry backup done prior to the errors occuring, I'd say it's time to backup and be prepared to re-install the OS. You do not have to do it right away but all I am suggesting is that you backup your critical files right away...
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