Have you tried a remount of the heatsink? Maybe you got some voids when you installed due to pulling away or lateral movement of heat sink or excessive thermal paste in some areas? I have the same heatsink though on a Q9550 and since a line of arctic silver 5 on the cap across my cores of would only contact the middle heatpipe (since it would spread out into the voids that the heat pipe runs through), i applied it the old school way, spreading a small amount on each pipe. Now I use Shin-Etsu.
You could always try a dual fan Push Pull config. I know you said it is near the rear exauhst fan but with the side open you are not getting any draw through the heatsink. There is a PWM 120mm fan made by arctic cooling that you can piggy back off one PWM connector so it could contol two heatsink fans together. Also a second sound source adds 3 db of noise, so you could buy a fan with a little different RPM so that they would not resonate at the same pitch.
You are using the PWM four pin plug on the MB for the fan aren't you? Without the 5v signal this PWM fan defaults to lowest speed. You can see the big X and writing on the fan when installed on heatsink right
I am moving to water cooling, have all the stuff just need to install, seems like you would have fun going with water too.