The NB/ system temp reading is not accurate or if it is, its not coming from the NB. 35-40c should feel cool to barely warm at best. It could be the VRMs or SB as they are always cool or barely warm. The bios, ET6, Speedfan ect. all read the same for what is supposed to be the NB.
Software programs are all over the place. most don't even say they're for the NB. you just get a temp1, temp2, etc type reading. You can pick up a cheap thermometer just about anywhere. Try coffee shops, wal-mart etc. they are used a lot for making espresso.
The chip is obviously covered and lining up with the cut out. lol.. Its the design and weight that makes it so inefficient. And as I've already stated, I used Arctic Silver Ceramique. When the new thermal pads arrive, I'll be switching to AS5
I wouldn't use AS5. It has silver in it. If you get too much it can get on other parts of the chip and cause problems. I use MX-4, but the ceramique is fine and not an issue for you.
I wouldn't use thermal pads on the chip either they can run 10C hotter easily. Use paste alone.
What happened with the copper heatsink? or is that is what is giving you problems?
also, the design is just right. It is common for chips to be made to run 60C all the time. It is a safe temperature. I'm sure it's the same reason you replaced your CPU cooler. It was running a little warm so you replaced it with better as you don't get an option for better stock cooler like MB offer. I know all of my Intel processors always have ran about 60C on normal load and around 70C on stress load.
Just because it is hot to your finger doesn't mean it is hot to the chip. They can withstand very high temperatures. They are not made of meat and start cooking at low temps. 100C for a lot of chips is not uncommon and a safe temp. heat wears things down over time from heating and cooling all of the time, but your computer will be out dated before that happens. This is why they charge much more for higher end boards. You get a $100 heatpipe cooler included.
Luck
-=Mark=-