At the technical symposium following the Athlon 64 launch, Mike Goddard, AMD Director of Technical Marketing of the firm's Computation Products Group, explained it in a way that it has left almost as many questions unanswered. But the long and the short of it is that Socket 940 requires a 6 to 9 layer motherboard and Socket 939 only requires a 4 layer design, making the motherboards much cheaper for chips using the latter.
Goddard is a seriously technical guy, he comes from a background of designing chips himself and knows a thing or two. He said that Socket 939 would allow later Athlon FX chips to use standard DDR memory rather than the current requirement for ECC registered DDR.
Source : The Inquirer