have you tried disconnecting the usb and using a midi cable only? could be a ground-loop problem.
The headphones you mention have a very low impedance, perhaps try with a high-impedance headphone to see if that makes any difference.
I did notice that the headphone output is not as clean as the main outputs, but noise with the volume turned down completely seems a bit much.
Then again, good headphones can make you go crazy for small sounds.
I remember doing band recordings on a houseboat converted to a studio once, and we noticed some strange clunk-clunk noise when you turned up the mic volumes rather high.
Turned out to be someone in the next boat doing his laundry.