Hi, If you have the Windows 98 CD or the install files somewhere, I would run setup.exe again. You will not lose any of your personal files and the re-install should correct the files in Windows 98 that seem to have got lost.
There is some very important steps missing here. If you wish to re-install Windows WITHOUT LOSING ANYTHING YOU MUST:
1-Make sure any Antivirus program and Firewall is shut down so that they do not startup at bootup.
2-Boot the machine from a power off state DIRECTLY TO the 98 Startup disk. If you boot from the HD
Windows will ( or at least may ) if not watched create a NEW Windows folder ( ie: Window001. ) and WILL NOT pick up any existing programs/data etc.
3-Run setup from the Win98 folder on the CD.
so that windows is re-installed into the EXISTING FOLDER.
When booting directly to the floppy this is not usually a problem but should be watched anyway.
It is usually better to also set the Video back to standard VGA.