For some unknown reason I could not backup a different course, with no mention of a glossary on it. I got the Moodle equivalent of the blue screen of death: "An error has ocurred" after "Output of User data"
I had a look and saw that there were no users in this course. Adding one user enabled me to backup the course. I seem to remember something that did not work when there are no students in a course. It may have been this. But anyway, if anyone else is developing a course for the future and wants to back it up but can't - try adding a user.