Lets start from the beginning..
So you bought an extra HDD lets called it HD2 and the original HD1. Is this correct?
Are the drives Sata or IDE/? Or a combination of both?
And the ONLY thing you did was add the second drive to the computer?
Have you tried making sure no disks/or usb drives are in the computer?
Have you checking Bios to make sure that HD1 is first (or second to dvd/cd drive)?
Have you tried checking the cables to HD1 and the motherboard to see if they are loose? What about the power to HD1?
Let me know if these fix your problem as adding a HDD to a computer will not corrupt/damage the original drive.
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~Just StopSpazzing~
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