I've been getting an error while trying to backup some of my courses (not all). After some trial and error, it appears that, on my system at least, backup cannot create a .zip file larger than 2GB (we use Moodle as a collaboration and design/development support website for interactive multimedia courseware - with all of our development support graphics/audio/viceo, some of our Moodle courses contain over 5GB of data!). To get around this problem, we simply move some of our course files into subdirectories under the /backupdata directory. Since Moodle's backup does not attempt to backup files under /backupdata directory, this reduces the size of the backup .zip file. As long as we keep the required size for this file under 2GB, backup works great (it now successfully backs up 89 courses to about 20GB of .zip files)!
If anyone knows how to get a RedHat Linux server with Apache to allow a .zip file over 2GB, please let me know.
P.S. When the backup failed (due to .zip file larger than 2GB) and displayed an "Error", temp files under /moodledata/temp were NOT deleted - eating up a lot of disk space. If your backup fails, you might want to check this directory and delete all subdirectories/files (I do so about once a month).