Sorry to say guys, but the bundle of wire you all seem to be focused on should pose no problems. They carry 12VDC to the Tortoises and ground only for the 24VDC relays. There are no track wires there.
There is a 120 V power cord, but I seriously doubt that is making a difference.
I'm kind of leaning toward the idea that the upper deck casting an earth ground "shadow" on the lower deck.
I still need to run the train around, but I haven't been downstairs the last two days, as I've been helping a local train club move. They have a huge 2 rail layout that has been in place for the last 30 years, and have to be out by the end of the month. You can read about it here.