Me again
Thought I would provide you with another update. Original issue returned again, when I was backing up/creating system image with the windows 7 utility. The issue then seemed to be constantly present whenever I wrote large amounts of data to either of my 3 internal discs.
I cast my mind back to how the issue disappeared last time, which was when I altered the bios setting, changing the CPU fan speed to full. The corsair h50 has 2 power sources. One for the pump and one for the fan.
I had a Titan fenrir laying around and thought I would give that a go. I installed the cooler and ran various tests to try and replicate the issue. It now seems to have gone again. I can now write to the HDD at a constant 100mb per second, with no windows not responding or complete system slow down.
Can I faulty CPU cooler cause this kind of behaviour? Everything else seems to work fine now I swapped the cooler. By changing the bios setting for the corsair h50 previously, the issue went temporarily. Now using a different cooler it has eradicated it again. Never experienced this kind of system behaviour before so it has been difficult to diagnose.