There are a few possibilities.
One is storage mode set-ups in the BIOS, older motherboards often offered various options for how the physical ports would be presented as logical controllers, some of which would disable some of the ports.
Another is that while in theory SATA is supposed to be backwards compatibile in practice some controllers had bugs which would prevent them working with faster drives. Some drives have a jumper to force the speed down which may help (but the ones I have seen on 6Gbps drives only let you force 3Gbps not 1.5Gbps).
Another is that the SATA ports on the board are simply broken. Old hardware does fail sometimes.
Ultimately you may find you have to use an add-in controller card if you can't get the on-board to work.
Is the BIOS already failing to recognize the drive or just your OS? – Bobby – 2010-06-14T10:15:14.170
Bios itself is failing to detect my SATA hard disk – Renjith G – 2010-06-14T10:48:56.990
No other replies yet? – Renjith G – 2010-06-14T18:00:16.877
Motherboard manufacturer and BIOS version would be helpful here. It could be a BIOS issue. – Zoot – 2010-10-18T02:05:45.387
Some bios's you have to enable the specific sata port for the drive before it will be recognized. Some early hybrid (Pata-Sata) boards have problems with Sata II drives, some hard drive manufacturers have a jumper to clock it back to Sata I. – Moab – 2010-10-18T03:09:50.427