It's a quad-core CPU with 24GB RAM,
Another thing to check might be the cooling -- possibly if the heatsink is not well connected and the cpu it gets too hot it throttles to a lower clock speed.
Check your powersavings settings too to make sure you're not running below what you think you should have.
But I'm sure you'd have spotted that by now.
It *feels* like something is interrupting the CPU and I've
pretty much ruled out all the local PC hardware by replacing it..
It might also be worth to try booting into a live CD or two see if they perform better, which would move suspicion to the OS.
Additionally: I've had issues with the Virgin router just locking up
and needing rebooting, or locking up on the cabled ethernet side but
being fine on wireless. When I put a cable router in between the
Virgin box and my home network, this issue seems to then start to
affect the cable router. That's what made me start looking at the
network initially.
Hm, sounds messy. Some googling suggests there are various folks with wired ethernet problems on their hub. Perhaps it's worth trying to switch that.