1. Error Message. No, I don't need the rest of the error messages at this time. That error message has nothing to do with the scandisk command options. At any rate it's not normal. This error message as well as your previous references to "bad command" or "bad filename" indicate missing system files or a "bad" environment after boot. If you're starting from a "working" Windows 98SE boot disk (floppy or CD), you shouldn't have any of these problems. They setup a "working" environment and you should be able to execute the basic programs from the boot floppy or CD.
2. Boot Device and Media. What I need to know is, what operating system and media are you booting from?
a. Are you starting from a Windows 98SE boot disk (floppy)?
b. Are you starting from a Windows 98SE boot disk (CD)?
c. Are you starting from the Windows 98SE setup CD? Not really the same thing as the "boot CD". I know, it's confusing.
d. Are you starting from suspect hard drive containing your Windows 98SE operating system (with missing files)?
3. Goal. What is your immediate goal? If saving your data files is the most important thing, you shouldn't be using the hard drive in the current environment. If your startup problems have been caused by a hardware problem, you could damage the file system and/or data files within it. As "patio" and "WillyW" have asserted, it would be best to recover the hard drive's data from a "working" computer system first, then fix the problem child.
If on the other hand, you're trying to recover the data in-place, you should be starting from a "working" boot disk. It doesn't sound like you are.