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Start Scandisk.
Select drive.
Check the 'Atuomatically Fix Errors Box".
Choose either Stabdard or Thorough. (Thorough makes Scandisk work harder, but it takes longer).
Click the Start button.
Those are the directions in the book I have, anyway.
When you are at the command line from the boot disk, type scandisk ? - it should show you a list of options you can enable when starting scandisk. I believe one of the options is to automatically fix errors.
Try starting Windows in safe mode and then run scan disk. It sounds like some process is running in the background while you're running scan disk. That is probably why it was hanging at 9% the first time you ran the scan.
Another trick is to create a DOS boot disk. I think you flip a check box on when you format a floppy to make one. Then copy the scandisk***** to that disk. Boot from the floppy, and run scandisk. There may be a command line option so it will automatically fix any errors, or it may do it by default. I can't remember, it's been a while since I've used windows 98.