You need to start with a computer that's nominally identical (same motherboard and processor, the same specification of disks etc). Then run some benchmarking tools with the same operating system build on each.
If the figures come up significantly different (more than say 5% to 10%) then you know that there is something odd with your computer. That could be anything from poor connection on a cable, to poor cooling, a problematic power supply... You'd really need to replace things one at a time (or swap them with something similar from another system) to find the fault.
If you can't find something identical, swap things one at a time (start with things you've got to hand that you know are good).
If you haven't already, check all the BIOS settings, particularly things like the RAM settings, are correct. Check too things like any thermal sensors to ensure that your system isn't being throttled because of heat.