Software Updater ran, restarted, booted from external FW HD for no reason??

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I did a Software Update yesterday and got the latest iWeb and Quicktime. I was then prompted to restart the computer, it restarted and for some reason used by backup external FW HD as the startup disc. The internal drive is, and has always been, the startup disc. While running from the backup drive, I went Startup Disk in System Prefs, selected the internal drive and restarted. It restarted from the internal drive perfectly. I recently ran Drive Genius on the internal and external drives and the permissions are repaired nightly when SuperDuper makes an overnight Smart Backup of my system... the internal drive on my iMac was just replaced by Apple less than a month ago. Can't figure why the internal drive wouldn't get used. Why might the system have randomly elected to use the external FW HD as the boot drive?
iMac G5   Mac OS X (10.4.6)  
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I don't have an answer for you, because I've never seen that behavior, but suggest that you unmount and power-off any external HDs while doing updates. That will preclude that from ever happening again.