Question: It was stated that you have 2-50amp & 1-100amp AGM House batteries.
Are they all connected in parallel or are they isolated from each other?
If connected together the older AGM may be dragging down the smaller ones.
Are the two 50 amp cells car batteries, hybrid or deep cycle type? AGM?
It threw up a flag for me when you said the two 50 amps reached full charge by the charger yet the 100 amp battery is still charging. I would think that they would all have to be isolated from each other in some manner for this to occur.