Perhaps a good test would be to boot into safe mode and see if the system interrupts run hot with such a minimal boot. Is that something you've already tried?
I was under the impression Task Manager showed high System interrupts CPU usage when booted normally. Perhaps that was another thread. Can you check to see what Task Manager shows for System interrupts in normal and safe mode? It should usually be around .1 percent and is not supposed to go much above 1 percent event when very busy.