Have you tried uninstalling - restarting - then installing 3dmark06 again? I had to do that once whenever i was getting less than half my FPS when using SLI. I went as far as disabling one card and I showed a 20fps increase by using 1 card over SLI. But once I uninstalled 3dmark06, restarted, then installed it again - all was well.
Your issue sounds related to the chipset PCI-E...not cpu.
CD- You are using the latest 501 beta?..from here
Thats a weird one for sure...all CPU options in BIOS are 'normal'? I have never heard of this sort of thing before, where Task Manager actually shows activity on the 'dead' cores...
Someone spiked your cpu cores with a ruphie! "Its date rape, in Kenstfield...More..at 11."