Mac Pro will not boot from cd or external drive

My Mac has an issue whith the boot drive, and I would like to format the drive and reinstall OS-X Mountain Lion and then use Time Machine to resore the Data. When I try to boot my Early 2009 Mac Pro (OS-X 10.8) using the option key, it loads the scrren that allows me to choose among the bootable drives. Once I choose either an external drive or CVD, it loads to the apple screen, stays there for about 5 minutes, then loads the OS on the main drive... Any ideas would be greatly appreciated.
Bill Mueller

At first I was just going to say it sounds like you have a bad optical drive, but then you had to go and say that it also won't boot from a HDD.
That just makes things a whole lot worse.
Start by removing the side cover and checking the RAM to see if any of the LEDs are lit up indicating bad RAM. Usually if there's any bad RAM found, it will just automatically disable that stick, but maybe yours isn't for some reason.
Look for any other LEDs that may be lit. Generally speaking, the only time you should see an LED (outside of the power LED) lit consistently is if there's a problem.
You should also see if you can get Apple Hardware Test to run, which may or may not find some problem.
But sorry to say, it's sounding very suspiciously like a bad logic board.
One other thing to try, is putting the SL drive into a different slot. So if you were putting it in slot 2, try slot 3 or 4. If you just have a bad SATA port, you might be able to just work around that until you get a new system.
If by chance this system is still under warranty, do not walk, do not pass go, do not collect $200, RUN to the nearest AASP or Apple store to make it THEIR problem to sort out.

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