CPU is probably core temp.
Since Sandy Bridge, CPUID states that the intel chips return one temp per core, plus a package temp... So package temp is not a mobo reading, but a temperature reported from the CPU itself. I forget what readings AMD provides piledriver, but I thought it was only one... So I don't know why you'd get different temps reported in the CPU and package fields.
The mainboard temp is probably reporting something outside of but around the socket, like the VRM area. This is my guess based off my experience with LN2 cooling... The socket area freezes pretty solid pretty quickly once the processor is down to -190. However the mainboard temp reading takes longer to creep down to subzero readings, which implies to me that the reading is being taken from somewhere on the board further away than the socket that takes longer to get frozen. Also, the mainboard temp gets considerably hotter when more voltage and load is applied when not subzero, which could imply that its a reading from the CPU power section... This is all just inference based on my testing and observing readings. I haven't actually read anything conclusive about where the sensor is.
My experience here is based on Asus mobos as those are what I've spent the most time on when looking at these kinds of temps. Mileage may vary as I don't know that sensor location for this is standardized.
