We upgraded our Ubuntu version and ended up having to rebuild the whole server. Bottom line, that meant we had to import old virtualmin backups into the brand new server.
Low and behold we got this same error.
Good news is we found a cure that worked for us. The “Website documents sub-directory” was blank. Once we put public_html in that box and hit save, boom, there was no error.
Hope that helps anyone else who gets this.