Chris
The Kona card should always be in the slot farthest from your video card (called slot 4) with the only exception being for users with SCSI. fibre or SAS storage, then that card needs to be in the #4 slot and the Kona card should then be in slot #3.
On PCIX machines the slot next to the graphics card should be unused.
On PCIe machines it would depend on which machine version + config. whether slot 2 would be usable or not.
gary adcock
Studio37
HD & Film Consultation
Post and Production Workflows
Inside look at the IoHD
