Question GTX 1060 6GB underperforming

Alright, this might sound weird. But here goes. I'm a bit baffled.

Specs:
Asus P5Q Deluxe
Intel Xeon X5470
Noctua NH-D14
Gigabyte Nvidia GTX 1060 6GB
16 GB DDR2 @876 MHz
Samsung 850 Evo 500 GB
HP EX950 1TB
x3 2.5" HDD 7200 RPM Striped Array 320 GB [1TB]
Antec Green 650W

Obviously this is an old computer. I know this, it's just a computer I put together for fun.

Before I was running this PC with same specs, except the Motherboard was an Asus Rampage Formula X48, and a Q9650.

I recently upgraded to the X5470 and the P5Q Deluxe.

At the same time as these upgrades, I also upgraded to the newest version of Windows released (Before 2004 though) and the newest drivers. I tried a DDU reinstall as well. No luck.

The X5470 is overclocked to 4.4 GHz [1.425v, 84C Max Temp, Prime 95, passed up to 6K, which is stable enough for me.]

The Memory is overclocked to 876 MHz from 667 MHz [2.00v, 7-7-7-28, successfully passed 2 iterations of Memtest86, which is stable enough for me.]

The Motherboard FSB is overclocked to 438 from 333. BIOS has been manually modified to include microcode for the X5470 processor.

I used PerformanceTest by Passmark, and it performed at about 7500 points when an average GTX 1060 6GB score is around 10000. I noticed some odd stuttering in games so thus began my investigation...
The graphics card performs normally in most applications. Only DirectX9 and DirectX12 seem to be performing abnormally. This same GPU performed normally with the old motherboard. MSI Afterburner does not display a BUS Limit reached, Power Limit Reached, Temp Limit Reached. CPU utilization is also not at 100% on any core in DirectX9 or DirectX12. It does however show that the GPU is being 100% utilized during these benchmarks.

In all actuality, this machine should be performing quite well despite it's age. I want to blame it on Windows, but honestly I'm unsure. All of the hardware checks out, and I am not getting any blue screens. No indication of any failure in software or hardware.

Thoughts?