My best guess is that the source of the problem is coil whine from the motherboard. i have tried replacing the PSU to no effect.
I think you're right.
Some Asus motherboards do exhibit this kind of behaviour, and no doubt other makes must do too.
I can however not hear it in a pair of headphones.
My Asus PC does the opposite.
It's clean through speakers but has that faint ghostly interference through headphones.
It´s also transfered if i connect from the onboard motherboard audio card straight to the amp.
Have you tried using a dedicated soundcard?
This is something I intend to try once I can figure out how to install it into the PC.
So many different cards, so many different motherboard sockets ...