Tip: When one of your engines are operating and batteries need a charge, you should see +13.6 V at the batteries. 6V GC2 golf cart batteries love + 14.6 V for charging but you will need to monitor electrolyte levels.
It may take awhile for a battery isolator to pass charging current from engine alternator to house batteries. The engine alternator needs to charge chassis battery after a cold start. Not knowing what exactly you have for hardware limits technical advice.
I may have missed this but you are using an adequate handheld meter for diagnosing all this?
