Yes, good point, perhaps the hard drive you are using needs to be set as the boot drive in your BIOS. If the system tries booting from another drive it won't find the operating system, and therefore the installation will begin again. To get into your BIOS, you usually have to press F8 or Delete during the boot (most systems will display an option). Try and find the option that allows you to set the order of the boot devices, and make sure that your hard drive which has the OS installed on it is set as the first boot device. If that doesn't work, what you suggested might be helpful - changing the jumpers. Make sure the "OS drive" is set as the Master.
If you can't find your way around the BIOS, write down the main menu options of your BIOS and post them here