We run a test site and a live site, we have tested going from both, and have to restore courses that blew up, so going from our live server to our live server. We have re-created another site with the same name plus one character to the name, placed the students in the course before doing the restore.
We have found that the default settings (Site Admin - Courses - Backups - General back up defaults) has to be checked as the default to include users. Whether or not you want them, This way on the back up you have the option of unchecking the box to not include users.
For some reason when the default was not to include the users, and we checked the box to include then do the back up, the gradebook would have errors instead of their grades.
We use Datatel to have that build courses and auto enrols students. We have found that the Students must be enrolled back into the course, for everything to work out smoothly.
Not sure if this is just our set up, but it is what has worked for us. In the "General back up defaults" we have everything checked except "Anonymise information"