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?