I think United Specialties wired my generator to the chassis batteries. Not to the coach batteries. That way I can use my house/coach batteries down to nothing and still start up the generator. Then when I start the generator it powers a recepticle in the storage bay that powers the charger/convertor and charges up the house batteries. There is a large rotary switch in that bay that allows me to use only the house batteries, or only the chassis batteries, or both sets if I want. My truck chassis has 3 truck batteries. The coach/house batteries are two 12v deep cycle ones. When I'm boondocking I set the switch to only use the house batteries. That way I can run them down and not risk draining the chassis batteries and not be able to start the generator or motor. When I'm under power or hooked up to shore power I switch the two battery systems together so the alternator or the charger/converter will charge up all batteries. Works pretty good that way I think. I wonder why they wired up your generator to the house/coach batteries?
'03 Freightliner FL112, 295" wheel base, with '03 United Specialties 26' living quarters, single screw, Cat C12 430 h/p 1650 torque, Eaton 10speed , 3.42 rear axle ratio