I too believe your output is just not getting to the batteries. First see what the voltage is on the engine battery. Idle up a bit. Then try to find the path to the chassis batteries.
If you want to prove it to yourself, just use a jump start cable from the engine battery to the chassis battery and you will see the voltage come up to the same level.
Whatever type of device in between is not working properly or you simply have poor connections.
Twelve volts has very little push factor and cannot go through much rust or corrosion.