we mainly use your X9SCL-F board with Adaptec 6405 controller. That worked okay.
But now we have the first Ivy-Bridge CPUs and updated a X9SCL-F board with the 2.0 bios. After the bios upgrade, the mainboard is unable to detect the raid controller. Before the bios update the same controller was detected okay.
Can you Change BIOS Menu \Integrated IO Configuration \PCI Express Port = Enabled.
This will fix the issue.