I recommend you take it to your radio installer. This is not part of the contract so it will cost you. The dealers are usually not capable of working on these systems.
You may want the EMS equipment provider to offer his input as well. 4 batteries is asking for difficulty, 2 large ones, space permitting, is a better way to go. It is probably diesel that should be taken into account. The on board charger must be designed for the batteries in question. Most vehicle alternators are not rated for AGM and may destroy one. GelCels are a lot more forgiving but they too can be destroyed by overcharging.
I don't recommend "isolators" even the ones with Schottky diodes, prevent the regulator from sensing the isolated battery, resulting in either over or under charging. If you must have an EMS bank and start bank you are better off using a 110 VAC inverter with a suitably sized charger to charge the EMS bank when underway. Many of these can charge multiple banks. The batteries must be of the same type though the size may vary. Starting batteries being smaller.
I installed this stuff for 30 + yrs starting with the "orange box" in the 70's.
There are a large number of variables, and with the protocols changing annually, it is difficult to troubleshoot from afar.
Something is not right, if everything is working properly, you shouldn't need to have it charging 24/7 though all of the services on LINY are usually plugged in unless they are on the road.
Let us know.
Jim W