I had the same problem, the fix was in the bios settings. I have a MSI motherboard and I do not know if the settings are the same for other boards but to fix it I had to go into the Integrated Peripherals settings and then the On-Chip IDE Configuration. For XP the On-Chip ATA(s) mode needed to be set to Native, the ATA Configuration to P-ATA Only, S-ATA Keep Enable to Yes, P-ATA Channel to Both and S-ATA Ports Definition to PO-1st / P1 - 2nd
You are having the problem probably because your bios is set only to recognize the SATA and not the IDE 1 and or 2 slots. You need to check you MoBo manual and/or call the manufacture to get help to have the MoBo see all the slots.