You need to set "First Display Init" to PEG. It's probably set to PCI.

I have the same exact setup the OP has. PhenomII X3 unlocked to X4 and Gigabyte GA-MA790GP UD4H. Disabled onboard video and using a 8400GS (rig is not for gaming, I just didn't want my system memory sucked up by the onboard GPU even though it has dedicated 128MB sideport mem). I had to set the First Display Init to PEG, then disable the onboard GPU. Works fine. Oh, Windows Vista 32.