I'm still hovering around the "window" button on the tailgate. I was thinking something wacky w/ the relay that's controlled by the fob. But that get's disabled when the ignition is on.
However, the lift glass can be opened from outside in any situation, (driving, parked, key on/off). The "button" and the glass latch are two seperate parts. Did they also change the button? If not, that's where I would look. If they did, I would still look there.
Check all the wires to and from the button and the latch mod for any sign of damage. It's the only thing that's active in all situations.