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The only thing I can think of is that with my server it's a problem related to the account being an Open Directory account. Maybe since it's not a local user account, the crontab is flushed whenever it logs out or the server is rebooted. I've set it up so SuperDuper is running from the local admin account (which was usually not logged in). If that solves the problem, my suspicion will be that my users are having trouble because they aren't following directions. They may be shutting the machine down, putting it to sleep, logging out, or something.
Along those lines, are there any plans to get SuperDuper's automated backups to run as a daemon so they will execute even if the user that configured them isn't logged in? This is pretty easy to do using a launchd job placed in /Library/LaunchDaemons. All you'd need is a headless version of SuperDuper to call with that job and make the backup.
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