registry checker

Windows registry checker comes up on every reboot. It tells me it has found an error in my system files and replaced it with a recent backup. It then repeats the process over and over until it tries to rebuild the registry and is unable to. I have to boot in DOS and manually replace the files with good backups that I have renamed to keep registry checker from deleting them in this process. I am running Windows 98 on an AMD K6-2 350 Mhz machine with 128 MB RAM. This happens whether or not I install any new software. Any way to keep this from happening?