Update: 12/20/2007
In the BIOS under "Advanced Chipset Features" -> "System Clocks" there will be an option that states "PCIe x16_3, MHz", this option sets the speed for PCIe slot number 3, which is the PCIe slot in the middle. PCIe x16_3 is PCI Express 1.1 compliant and is controlled by the MCP (southbridge).