That same thing does happen to me too. in a video that i saw explains how the processors work, so in a quad core CPU, obviously there are in a total of 4 cores. But the active once will be 2, and the other 2 would be acting as the backup cores whenever one of the main core is disabled. this is setup by the manufacturer so that there will be less complaints about slowing down of the system.
so that could be the reason why the tempts of the cores are different. but i wont say that i m sure, maybe you should seek help from where you purchased your PC, or any manufacturer