I have been lucky a couple of times letting scandisk run on the drive from DOS. If it has anything to do with screwed up files..chances are scandisk can fix it. If you can get into Win98 in safe mode, you can run SFC (System File Checker) from the start > run menu...which will find missing/corrupt files and allow you to replace them from your Win98CD.
You can get a Win98 boot disk with scandisk (plus other good utilities) from
http://www.bootdisk.com/ ... click on the top listing: DOS - Windows 9X/Me/NT/2K/XP Excellent "
bootdisks" and on the next page, download (1) Windows 98 Custom, No Ramdrive or (2) Windows 98 SE Custom, No Ramdrive.
These will be executable files. Place a formatted diskette in your A: drive and click open the executable (either boot98c.exe or boot98sc.exe) that will execute onto the floppy disk and create the bootable floppy. You now leave the diskette in the A: drive and boot. This will take you to an A:\> prompt where you will type scandisk C: <enter> Scandisk will run on the C: drive (I am assuming your Windows 98 is on the C: drive) and it will find any errors and ask you if you wish to correct them...say yes. It will also tell you that it is going to make changes to your drive..do you want to save the data. I never do, but you may want to...it can be saved to the root of C: or maybe a floppy diskette.