Well, you seem to have the solution to your own problem, you just didn't realize it. The system is designed to maintain the temps at proper levels, 50C is pretty normal and so the fan (PWM Fan) works at it's required speed to keep the temp normal. If your processor should go beyond 80C then I think you'll see the RPM go up that High, although, I still have never seen or heard a 6000RPM fan, I'd be pretty scared for I bought a PC not a RC Copter..... would hate to see my rig lift off.
One thing is for sure my rigs at 44C with a 1200 RPM, so you do need a new HSF for that rig.