Like the post before, make sure you have enough fans for cooling. My current setup is a quad core with a beast of a motherboard and graphics card. I have 2 fans on the case and the CPU and GPU both have there own fans. The case has mesh at the front and lots of side inlets. I have found that this works perfectly even under stress but if you want to overclock, you may want more/better fans.
Particularly in your case, the fans may not actually be running at the speed whatever program you used says.
Also like the post above, tie some cables up to improve airflow.