I discovered the same thing a couple years ago. The switches with the built in charge ports do not disconnect all the wires going from the battery to the receiver. It disconnects only the positive wire. All receivers have a common negative bus. All the negative polls are connected. When you try and charge both batteries, the 2 charge circuits are connected. The charger is fighting itself, cannot read a separate battery and will give false charging. You have to charge them one at a time or disconnect them from the switch to charge at the same time.
At least, this is how it was explained to me.