A mistake most people make is determining how quickly batteries charge and discharge. People think if you put a battery on a charger it should be charged up within an hour. This is false. Depending on the level of discharge, it might take several hours or even overnight to charge it fully. Also, a partially charged battery will discharge much faster than a fully charged battery. So, if you put it on the charger for an hour and then attempt to use it, it will discharge again very quickly.
From your description, it sounds like your genset issue is directly related to your battery problem. One thing that you said that is questionable is that your genset is under warranty. Do you have an extended warranty, is your rig new what? If your rig is new then why did you replace your batteries? Generally, batteries will start their charging around 15VDC and then that will drop slowly as the battery reaches it's full capacity. AGMS are different than wets also, so your on board charger needs to be told they're AGMS....Dennis
The following article might help answer some of your questions. At the very least, it will give you a little insight. Click
HERE BOL...D