I tried to backup using the CLI approach and ran into the same problem. This time it is very easy for me to find the actual backup folder and log because I had deleted everything. So, I have included the folder and the empty log file in a zip file in this message if that is useful in this process.
Having had a look at the contents of the folder, I see that it seemed to correctly create an xml file for the course (see /course/course.xml file) but it did not finish making the /course/enrolments.xml file as it is empty. So perhaps this is a clue if it stopped at that point between making the course and the enrolments files.
Interestingly now that I'm looking at the folder again on the server, I see that Moodle has graciously created about 40 other folders for backing up. So there must be some mechanism that is going haywire behind the scenes and still executing somehow.