Yes, it should work fine. As long as you keep the original HDD in the computer at the same jumper settings, there shouldn't be any problems. Make sure to install the second HDD with the correct jumper settings. Like you suggested, the jumper settings and cable settings are the most probable problem. In some computers, even after installing the new HDD correctly, you have to go into BIOS and select the HDD Auto-Detect feature. This will search for new HDDs and keep them in the BIOS settings after it detects it.
What is your original HDD set as on the cable? If it's set on the Primary IDE cable as Master, then I'd put the new HDD on the same cable as Primary Slave.
-Lasereth
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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