This is a problem. Some people are overclocking and thinking their temps are ok, and they are not.
I use TAT (Intel thermal analysis tool) and coretemp. They only differ by 1 degree at the most on my system.
However my Gigabyte bios and Gigabyte hardware monitoring software (easy tune 5?) both show the temperature much, much lower than what it really is.
Similar problem here with a Gigabyte DS3 mobo. Easy Tune & Core Temp have the same readings, and TAT is about 10°C higher.