I'm no expert and am currently having my own temp dilemma, but I doubt your bios is that far off. It has to be the way you mounted the cooler. You should be using all 4 screws. For all you know when tightening it down all the paste squeezed over to the side without a screw. I'm guessing if you installed real temp it would show one core sky high and your other cores may be cooler.
Bottom line, you cannot trust your cooler to work properly when it isn't mounted properly. I suggest you re-seat the cooler and use all the screws. If that's impossible for some reason get a different cooler, or use the stock cooler until you can purchase another one.