How quickly does the temperature rise? If it's really quickly then that might point to a contact issue. If it's really slowly then it's about overall cooling.
The temperature rises immediately. So in that case I should try the lower spacers? The Twin Turbo comes with two highs for spacers. The GTX 680 wasn't listed, so I guessed I would need to use the taller one since a lot of other nVidia GTX cards used the taller spacers.
When using the Arctic Cooling's fans, what RPM were they running up to? They should have been going full speed if the cards fan control was working properly. What about ramping up the airflow and just seeing what difference it makes? 2x800rpm 120mm's should move close to 200W without much problem but it might be worth speeding them up?
The fans do not go through the fan controller, they are plugged directly into the PSU, and running full speed at 800 RPM. They are fixed speed fans, not PWM.
Also how is your system built? Much cooling around the graphics card area?
I have the Fractal-Design R3 with a side panel fan, that isn't currently plugged in.
Edit: Also which direction should the fans be pointing? Pulling the air from the VGA or pushing? I seem to be getting better temps from a pull configuration...