If you want to identify if it's clearance issues, it should be fairly simple. Using something like Kapton tape, tape the tops of the gearboxes and under the rollers where they'd meet the frame.
To be honest, I'll be a little surprised if this is the issue, I measure over 3mm clearance from the gearboxes to the rail of a perfectly flat piece of track. If you have a center rail that projects that much higher then the outside rails, I can't imagine that it would be only the BEEP that would have a problem. I'd be looking for other causes, one being there are only four wheels, and one has a traction tire. I see wheel sparking over my double-slip switches with small motorized equipment, most likely because of limited outside rail conductivity.