Way to guarantee start-up from main disk?

Using OS 10.6.8 on a MacPro, I use SuperDuper to daily back-up and make a clone of my main Hard Drive to another internal Hard Drive. I also schedule my computer to automatically start up every morning. The problem is nine time out of ten the computer starts up from the main drive but occasionally it will boot from the clone. If I don't catch it, things can get messy real fast as I start altering what are essentially backed-up files.
So, the question: is there a way to insure the computer always, without fail, boots up from the main drive?

The only thing that could explain this behavior then is for some reason the backup is somehow coming on line before you primary drive and being found as the only available drive to boot from at the time it is needed.  I would check the drives with Disk Utility and maybe move them to a different bay just to experiment.
By the way, instead of shutting down I recommend you just sleep your machine.  That's what I do.  Daily it wakes up to do it's backup and then goes back to sleep.  Everything is basically off anyhow when the mac pro sleeps.  No fans, no drives.  And then there is no need to boot when you need the machine.

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