After checking my system log, it seems that coreaudiod crashed just before the cron started at about 3:15 am. I don't think I was using my machine at that time. I tried VLC again with the same files and it seemed to be ok. Does anyone know how to restart a root process like coreaudiod without rebooting?
Ok, I've discovered that if you just quit the process, it asks to authenticate and the daemon reboots fine.