I was wondering if anybody knows of a way to workaround this, or fix it
You can run a utility that checks and fixes your hard drive from DOS. You'd need a Windows 98 boot floppy disk (or maybe some other kind of DOS disk, all I know is that my Win98 boot disk has it) and a floppy drive (you can buy an external drive which connects by USB if you don't have an internal floppy drive).