Welcome, Newcomer. Your problem is a little unclear. IF Windows does recognize the HDD, that means so does the BIOS. Windows XP and earlier do not have native SATA drivers; you must install the SATA drivers when the installtion prompts you to press F6 to add third party or RAID drivers.
To make this dilema manageable, mobo manufacturers (the BIOS writers, actually) have installed IDE emulation via SATA ports. This is sometimes called Legacy IDE or compatability mode. However, this mode is not always the default setting because of Vista and 7. Ensure that you aren't using AHCI mode in the BIOS.