I don't have a cpu fan to molex adapter, so I just put in another fan I had from my last CPU to test and see if it was the fan at fault.
This other fan is having the same problem. Just won't speed up to cool the cpu down. Q-Fan does absolutely nothing.
Could this be something to do with the new CPU needing more voltage? Can I set this in the jumperfree configuration in the bios? It has settings for CPU voltage, but I'm inexperienced with CPU's/voltages and afraid to change anything without proper advice.
After much troubleshooting and frustration, I had the whole computer set up and running outside of the case and the CPU fan was running at 3500RPM average and CPU temp dropped right to 30c.
I then tested it playing a CPU intensive game (FIFA 12) and the CPU only went to 38c and the CPU fan RPM went up to keep it cool! It was usually going up to around 70c before with the 975RPM.
So that lead me to believe it was something in the case interfering with the fans voltage from the four pin power on the mobo.
So, I put the whole thing back in it's case in same set up as I had just had it working and low and behold the fans RPM was back down and the CPU was running hot.
Figuring the only thing that was different from outside the case to inside the case was the fact there is screws now touching the mobo, I decided to take them out one by one, booting up each time with one less screw, to see if was them. Starting logically with the screw closest to the cpu fans power pins, I hit the jackpot. It was that little bar steward causing some kind of voltage problem. I have it running now inside the case at a cool 32c and fan speed of 3169RPM.
Also, the fact I removed the CPU a couple of times and completely messed up the thermal paste is encouraging to still have a cool CPU. So hopefully when I re-do the thermal paste properly it will be even cooler.