This is the ECS K7S5A, in the sig, and not something else?
It carries the standard audio on the backplate, not on a riser, which rules out a faulty riser.
I'm clutching at straws now... are all the motherboard mountings accounted for? - if one is where it doesn't match up, then it could be shorting something - though it would be sheer luck for it to be no more than one audio channel.
The speakers have been changed, the motherboard has been changed, Windows reinstalled, what else is there?
The case and backplate, presumably are not fouling the plug, preventing proper insertion.
There's a FP-Audio connection - are there jumpers to switch to it, or jumpers to enable/disable the headphone amplifier, and could they be wrong on all the motherboards? - if a batch was mis-assembled, they could be!