How have you connected the new harddrive to your motherboard?
To a regular IDE channel? If so, to a channel where there were another drive present? Check to make sure that the master drive (the original) is set to master with slave present and that the new drive is set to slave.
To a RAID controller IDE channel? If so, enter the RAID setup menu (after the regular BIOS) and chose something along the lines of "Automaticly create RAID 0(+1)" and install the RAID drivers in windows.
Hope this helps, if not, we'll need more info