Do you use the same ground for both measurements?
Different rails can have different ground levels, could be one explaination.
The vgpu ground plane can also float a little.

Try to measure the voltages in reference to the PCI-E ground on each card, and also compare them to the motherboard ground (screw holes and such).

Another thing I have noticed is that some voltage regulators use the 3.3V rail as a referens voltage. (A P5W64 overvolts the vcore higher with higher +3.3V for example) There might be a droop on the 3.3V voltage to the PCI-E ports on one of the boards.