I have got the same thing going on with my late model Mark IV. When I am groovin' on an open G chord, I get that same ringing in the background of the chord. I have swapped out all of the preamp tubes one-by-one with no change in the ringing. I play Strats - Although, one has a HB in the bridge.
The only thing that I have found to stop the ringing was to put an improvised rubber string damper behind the nut on my guitar. And the problem seems to isolated to the open G-string. Without the home made damper, I can get the chord ringing and the ghost note starts up, I take my right index finger when I here the ringing, touch the G-string behind the nut and the ringing stops.
I would sure like to know what it would take to kill the ghost note. But I would also hate to change to different tubes because I REALLY like my sound these days... And it took me a while to like my Mark IV this much!
Brett