Answered my own question on this, the hard way!
Under loads ranging from idle to Portal 2 that #4 position was consistently 15-20 degrees Celsius hotter than anywhere else on the board even though it had a top-end Corsair water cooler on it and lots of fans elsewhere and it was never stressed. Other than Portal 2 - which doesn't seem to work the machine very hard - I do documents and spreadsheets!
And the board eventually blew up, will be going back to Gigabyte for warranty. Twice, on cold startup in the morning, the system BIOS lost its brains, could not access boot devices, had to reflash BIOS.
The same CPU, and the same water cooler, are now on an Asus Maximus VIII Extreme board and the CPU temp and all other temps at idle are hovering in the low 30's.
The temperature disparity on the Gibabyte board was there from the beginning. It seems likely that as I feared it was a warning sign of a problem with the board.