I've made some progress in narrowing down where the problem is. I did a full MySQL dump of the course and imported it into a new Moodle on a different server. From this new server I can backup individual courses without corruption. It's a bit of a long way to get a backup and to be able to re-use courses, but at least it works. I'd still like to know exactly what the original server is doing to my files though.
JE
PS I've now narrowed it down further. It's the restore function which isn't working properly rather than the backup. The new Moodle (on a Win2003 machine in my office) restores the backup file, the old Moodle (Linux, hosted) corrupts it.
Backup and restore
Backup corrupting lessons
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