Hi,
So I thought I'd run the MSI Afterburner test before reinstalling the cooler and according to it the CPU didn't fall below 100% usage at all? Also on the Heavyload test the graph there didn't show any problems but the task manager was still showing the cycle on all individual cores. I ran Prime95 with the same results.
Is it possible that the fan (with its speeding up and down) and CPU reading in task manager are faulty?