Then you never used all cores for calulating for a longer time. I had a setup like you for around three months.
The problem: When all cores are working, CPU-Pack-A is getting hotter, but not the Northbridge. The fans does not react to this situation, the CPU-Pack-A goes up to over 90°C and start with throttling.
Meanwhile Mac Fan Pro is thinking: Oh, the Northbridge is pretty cool, Booster-A can stay at 799 and Intake at 1200. Ok, the Exhaust speed up, but this is not good like Booster-A and Exhaust together and i would say it is much louder.