I'm confident this is what's wrong; The 4 SATA ports are not using the same controller.
Must Read the Manual
p.5-2 (p.108) Promise & Via controllers
p.1-2 (p.16) Dual Serial ATA RAID
p.3-1 (p.25)
Need to find the correct ports for the Via controller
p.2-24 (p.46) You want the Via SATA ports shown in the picture. (the pair on top of one another, marked SATA1, SATA2)
p.2-25 (p.7) You do not want these, they are for the Promise RAID. (the pair side by side, marked PRI_SATA, SEC_SATA).
This would explain why it's not showing up in the BIOS where you expect it. It won't, if plugged into the Promise.
Motherboard even has an ATA RAID connector. I have an add-in PCI card in an old PIII Asus that is very similar, 1-ATA, 2-SATA.
Your Asus is a transitional motherboard, a very early SATA-150 & when large hard drives were under 160GB, so RAID was a viable option.