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i believe the pentium d's have cpu stepping, so when running cpuz you'll see it throttle down when it's not being utilized. i THINK you can disable this in your bios if it bothers you, but that really shouldn't effect your gaming performance.
page 1-16 of your mother board manual has recommended memory manufacturers. is what you have one of those ?
also.. you have pc 5300 which runs at 667hmz, your manual recommends pc4200 (533mhz), perhaps this might be where your problem is ? i have an old intel motherboard that is a complete bitch about memory AND timings.
for now, i'd leave your heatsink on, as suggested before check the temperature in the bios, but if you're actually making it all the way 3dmark05 i doubt your cpu is over heating.
is your bios up to date ?
motherboard drivers ? chipset (via), sata, usb ?
How about i use Omega instead of the ATI ones? I'll firstly have to clean heatsink and rebuild OS but can try that after
PS. i always do motherboard drivers before anything else. Also, i'm using like a ASUS 600 driver, which was released in 2006, so i think its pretty up to date.