Header CN9 controls PCI-X Slot 5 setting. When CN9 is open, no jumper, slot 5 is set to 133MHz. When CN9 is on, slot 5 is set to 100MHz. The frequencies describe here are maximum operating frequencies. If PCI-X channel is shared with other devices, then maximum operating frequency cannot be achieved.
Refer to the following diagram for the location of CN9.