A few things first. You need to verify that the dual bank setup is operating correctly. This would be confirmed with a known good digital volt/ohm multi-meter. You want to test for alternator charge to both battery banks, when its supposed to be there.

Next, what is the static (at rest) voltage and engine running voltage, of both batteries? If the static voltage is low, then you first need to attempt to charge the battery. Then let the surface charge dissipate, then remeasure voltage. You let the freshly charged battery sit for a few hours, or depending on your switch setup, do 2 to 3 10 second cranks of the engine. Or turn the stereo on for about 15-20 minutes. a good used battery should rest at at least 12.5V.

Three-Wire Calibratable DC 0~30V Blue Digital Mini Voltmeter Gauge Tester
This is an instant red flag for me. For testing, you need to be sure your equipment is not lying to you.