This is more likely to be the scanner software, didn't you get a disk with the scanner?
You don't need to reinstall Win 98se.
This is my suggestion: (assuming USB scanner)
Unplug the scanner from the pc, go to add/remove programms and uninstall the scanner.
Restart your pc and reinstall the scanner software then plug the scanner back in.
That way you wont lose any files.
If you don't have a disk there's a huge range of drivers at click here