Is that 39C at load or idle? I'm assuming at idle, since you mentioned your video card is at 32. In that case, that is pretty high. How much more then your room temperature is it getting (the delta is a much better indicator of how well your cooling is working).
You may want to re-mount your cpu cooler. The good thing about the apogee XT is that the tension springs are pretty much preset, so you can screw them down as far as they go. If it were me, i'd clean off the chip to a nice shiny top again, and reapply my thermal, and remount. Since your using AS5, my person preference is to take a sandwich bag or ziptop, turn it inside out, and use that to smooth the thermal with my finger. There's different schools of thought on that, but I find I get a nice thin coat when I do it that way.
You may want to re-mount your cpu cooler. The good thing about the apogee XT is that the tension springs are pretty much preset, so you can screw them down as far as they go. If it were me, i'd clean off the chip to a nice shiny top again, and reapply my thermal, and remount. Since your using AS5, my person preference is to take a sandwich bag or ziptop, turn it inside out, and use that to smooth the thermal with my finger. There's different schools of thought on that, but I find I get a nice thin coat when I do it that way.