CapDave,
The only issues we have found with interference with our ignition system have all been traced back to loose connections at the plug cap. You mention that has been checked and confirmed so I'll ask a few more questions.
How close are the batteries mounted to each other?
Are the power wires from the batteries completely clear of each other or do they share some of the same routing?
Are the switches co-located or on separate sides of the fuselage?
Just a few thoughts ... love to hear your responses.
Pete