Everything that we store on CodeGuard is compressed and then encrypted, and you are measured upon the compressed storage amount. This is likely the reason for the difference between your live hosted site and the content in our systems.
This could also happen because of excluded directories. By default, CodeGuard tries to exclude caches and temporary files from being backed up.
If you are still not convinced that not everything you want is being backed up, you can verify that we have all of your content by downloading a zip file of your contents and then comparing that with your live site, or you can use our Browse Backup Contents feature. If you are still having trouble, email us at CodeGuard Support.