I found the problem. After running a few different backups, I decided to really take a good look at the file struction. There were folders inside the IIS directory that had no name. Then, underneath that, it have many sub directories with weird names. Looked like either a hacker, or trojan, had once accessed the site and left reminents behind. After running dir /x /a, I was able to remove the bad directories and the errors in BE went away.
Thank you for trying to assist. Next time I will be more diligent at looking through the file structure.