I'm using the Asus P6X58D Premium, for some reason it doesn't detect anything plugged into the standard SATA. But if I plug anything into the SATA 6Gb/s it recognizes it just fine. This is the same with hard drives or optical drives. Any ideas?
Are you familiar with BIOS? It may be as simple as needing to enable those ports.
A more obscure possibility: See if the drives are seen in the BIOS, but not seen in the OS. A good-chance possibility for this is that those ports are set to AHCI mode and the OS has the IDE mode drivers. That's an interesting issue that I went through with an existing XP install when I wanted to switch to AHCI mode so I could do hot-plugging.
Let us know what you see in the BIOS, and we can go on from there. Have you tried plugging the _same_ drive, with the _same_ cable, into both connections and seen it in one / not seen it in the other?