I am having a problem with a P965/ICH8R chipset board and FC5 32bit. The first two SATA ports work no problem but the last two will not work. The ports show up in dmesg but appear that no HDD are connected to them. I have confirmed that this is not bad HDDs by swapping the drives around. If the drive is connected to SATA port 1 or 2 it works if I them swap the same drive to port 3 or 4 it will not work. The drives show up in BIOS post screen so are being seen at boot. As I said above the first two ports work with no problems at all. You can see from the dmesg below that the kernel thinks the the SATA link is down on these ports (ATA3 & ATA4) when there are drives connected to these ports.
The ICH8R is set to AHCI mode and all the ports are on the ICH8R south bridge i.e. they are not on a secondary SATA controller. I have this FC5 system updated and running the latest kernel available.
Thanks in advance for any advise.