Boot Drive failed to be found - Question Marks ???

I recently used SuperDuper to clone my primary OSX 10.4 Tiger startup disk to a second internal hard drive in my Intel MacPro, and now I am experiencing strange behavior when booting from the Cloned drive...
To start with, let me first say that upoin successfully cloning my main OS onto the secondary internal drive, I removed my primary drive from my machine and replaced it with a cleanly formatted blank drive for data storage...in other words, there is currently only one capable startup disk in my machine at the moment...
So when running my OS from my new Clone OS drive, everything works fine when the OS is running, and things are fine and dandy...When I restart my computer, the machine loads right back up as if everything is totally normal and functioning perfect.
But then I went ahead and shutdown the machine for a short while, and upon returning and attempting to power up again, the startup process brings me to the FLASHING QUESTION MARK icon shortly after hitting the power button (as if for one reason or another, its not seeing my OS)...
The only way I can get the machine to work again, is by force-quitting the flashing question mark screen thereby powering back down; then restarting holding the 'option' key, and choosing my Clone boot drive from the list of startup discs (as it does show up as the only available drive in this list...)...Then my computer loads back up again, and things are working as normal, again, as if there were no problems...I test restarting a few times - no problem...I then re-test shutting down and powering back on again...QUESTIONS MARKS AGAIN!!
Anyone have any idea what the heck is going on, and how I should go about handling this?
any suggestions would be greatly appreciated... Thanks!

Are you sure you have the startup disk set correctly in System Preferences -> Startup Disk?
If so, try zapping the PRAM. Reboot while holding down command-option-p-r. Continue holding them down until after the third startup bong, then release. After the Mac boots, try setting the prefs again and see if it sticks then.
If not, I suspect you might have a dead PRAM battery. Try shutting your Mac down, then disconnect the power cord and the internet. Reconnect the power cord but leave the internet disconnected. Boot the Mac. If your time and date is set to sometime last century, you need a new PRAM battery.

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