Well, I do run for extended periods. But definitely not THAT long. I usually shutdown the computer with the hardware button, might somehow interrupt backups?
I see a potential new feature here. Allow user to specify auto-backup interval (daily, weekly, etc.) and time of day when backup should be performed. If scheduled backup is missed because MediaCenter was not running at scheduled time, perform backup at startup. The UI for this could be added to Options -> Library & Folders, which is kind of empty currently :-)