Cant reinstall SYS files

[needhelp]

I want to reinstall the sys files on my hard drive. I have booted with the 98 boot disk (OS is Win 98se) I go to the a: prompt and type SYS C: as usual and all I get is the message that this is a bad command or file name. What is going wrong or what am I doing wrong. The computer that I am trying to reinstall the sys files to is working okay except at boot up it comes up on the screen that there is an error in the configuration system files and to run configuration program. And then it pauses with a message to press F1 to continue or F2 to go into set up. If I press F1 the comnputer boots normally and there is no problem. If I go into set-up I can see no problem in there. I have tried loading earlier settings but that doesn't make any difference. Why doesn't the sistem files install when I type sys c:
Any ideas? The computer runs okay but its very annoying. I have tried 2 windows 98 boot disks and still get the same problem

[homer15]

i'm trying to remember, but does the 98 boot disk have the sys command on it? i don't think it does, but i'm not 100% sure.

[reboot]

Yes, the 98 boot disk does have the sys command, although it may be loaded into the ramdrive...check the path to D: or E: and see if it's there.
I would run fdisk /mbr first, then sys and see if that works.