You have forgotten to say which ESD protection (D600-D601-D603 diodes) ic has the low measurements.
And which type motherboard you have.

In any case, It could be a defective ESD protection ic, bad print track to/from the cpu, or some damage to the cpu pins, or bad cpu solder ball.
The only way to measure it is to remove the ic with the wrong measurements, and measure it without.
Most of the connections are going to the cpu and the ESD protection diodes.

6.4v question, could be due another type motherboard with newer, different dc to dc (8 pins) ic's.
These measurements are made from a older type motherboard with 16 pins (3850/N5212) dc to dc ic's.
Or, your multimeter is not accurate, or your Dc to Dc 5v ic has some issues.
Nevertheless normally it should be 5vdc.